data_bmse000398 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmse000398 _Entry.Title Methylmalonic _Entry.Version_type update _Entry.Submission_date 2008-02-01 _Entry.Accession_date 2008-02-01 _Entry.Last_release_date 2012-10-17 _Entry.Original_release_date 2008-02-01 _Entry.Origination author _Entry.NMR_STAR_version 3.1.1.7 _Entry.Original_NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.DOI 10.13018/BMSE000398 _Entry.BMRB_internal_directory_name Methylmalonic_acid loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.Middle_initials _Entry_author.Entry_ID 1 Qiu Cui ? bmse000398 2 Ian Lewis ? bmse000398 3 Francisca Jofre ? bmse000398 4 Mark Anderson E. bmse000398 5 John Markley L. bmse000398 stop_ loop_ _Entry_src.ID _Entry_src.Project_name _Entry_src.Organization_full_name _Entry_src.Organization_initials _Entry_src.Entry_ID 1 metabolomics 'Madison Metabolomics Consortium' MMC bmse000398 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID assigned_chemical_shifts 1 bmse000398 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID '13C chemical shifts' 4 bmse000398 '1H chemical shifts' 4 bmse000398 stop_ loop_ _Release.Release_number _Release.Format_type _Release.Format_version _Release.Date _Release.Submission_date _Release.Type _Release.Author _Release.Detail _Release.Entry_ID 1 . . 2008-02-01 2008-02-01 original BMRB 'Original spectra from MMC' bmse000398 2 . . 2008-02-28 2008-02-01 update BMRB 'Fixed mismatch between software ids and framecodes' bmse000398 3 . . 2008-04-29 2008-02-01 update Author 'Assignments, 13C transition lists, 1H transition lists by Francisca Jofre' bmse000398 4 . . 2008-07-09 2008-02-01 update BMRB 'fixed misplaced 2D coordinates' bmse000398 5 . . 2008-10-21 2008-02-01 update BMRB 'Fixed IUPAC erroneous IUPAC names' bmse000398 6 . . 2008-10-21 2008-02-01 update BMRB 'Added assembly and entity information' bmse000398 7 . . 2008-10-28 2008-02-01 update BMRB 'added image and structure file paths' bmse000398 8 . . 2008-11-03 2008-02-01 update BMRB 'Altered tag names due to dictionary update' bmse000398 9 . . 2009-07-20 2008-02-01 update BMRB 'Updated the InChI string to match PubChem' bmse000398 10 . . 2010-11-11 2008-02-01 update BMRB 'Reset sweep widths to those found in parameter files' bmse000398 11 . . 2010-11-30 2008-02-01 update BMRB 'Added 1 PDB ID to Chem_comp_db_link' bmse000398 12 . . 2011-03-04 2008-02-01 update BMRB 'Fixed peak list ID issue' bmse000398 13 . . 2011-04-04 2008-02-01 update BMRB 'Added Provenance tag to chem_comp' bmse000398 14 . . 2011-04-11 2008-02-01 update BMRB 'Moved Dept 135 phase val info from _Peak_general_char to _Peak_char' bmse000398 15 . . 2011-09-09 2008-02-01 update BMRB 'Brought up to date with latest Dictionary' bmse000398 16 . . 2011-09-21 2008-02-01 update BMRB 'Standardized Experiment_file data paths' bmse000398 17 . . 2011-09-21 2008-02-01 update BMRB 'Added base dir to data file path' bmse000398 18 . . 2011-12-14 2008-02-01 update BMRB 'Set Assembly.Name to match Chem_comp.name' bmse000398 19 . . 2012-09-13 2008-02-01 update BMRB 'Added PubChem SID 85165190 to database loop' bmse000398 20 . . 2012-10-17 2008-02-01 update BMRB 'Set all _Chem_comp_SMILES Types to lower case' bmse000398 21 . . 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmse000398 22 . . 2017-12-19 2017-10-12 update BMRB 'InChI numbering updated according to ALATIS' bmse000398 stop_ save_ ############### # Citations # ############### save_citation_1 _Citation.Sf_category citations _Citation.Sf_framecode citation_1 _Citation.Entry_ID bmse000398 _Citation.ID 1 _Citation.Class 'reference citation' _Citation.PubMed_ID 17170002 _Citation.Title 'Database resources of the National Center for Biotechnology Information.' _Citation.Status published _Citation.Type internet _Citation.WWW_URL http://pubchem.ncbi.nlm.nih.gov/ _Citation.Year 2006 loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Entry_ID _Citation_author.Citation_ID 1 D. Wheeler D. L. bmse000398 1 2 T. Barrett T. ? bmse000398 1 3 D. Benson D. A. bmse000398 1 4 S. Bryant S. H. bmse000398 1 5 K. Canese K. ? bmse000398 1 6 V. Chetvenin V. ? bmse000398 1 7 D. Church D. M. bmse000398 1 8 M. DiCuccio M. ? bmse000398 1 9 R. Edgar R. ? bmse000398 1 10 S. Federhen S. ? bmse000398 1 11 L. Geer L. Y. bmse000398 1 12 W. Helmberg W. ? bmse000398 1 13 Y. Kapustin Y. ? bmse000398 1 14 D. Kenton D. L. bmse000398 1 15 O. Khovayko O. ? bmse000398 1 16 D. Lipman D. J. bmse000398 1 17 T. Madden T. L. bmse000398 1 18 D. Maglott D. R. bmse000398 1 19 J. Ostell J. ? bmse000398 1 20 K. Pruitt K. D. bmse000398 1 21 G. Schuler G. D. bmse000398 1 22 L. Schriml L. M. bmse000398 1 23 E. Sequeira E. ? bmse000398 1 24 S. Sherry S. T. bmse000398 1 25 K. Sirotkin K. ? bmse000398 1 26 A. Souvorov A. ? bmse000398 1 27 G. Starchenko G. ? bmse000398 1 28 T. Suzek T. O. bmse000398 1 29 R. Tatusov R. ? bmse000398 1 30 T. Tatusova T. A. bmse000398 1 31 L. Bagner L. ? bmse000398 1 32 E. Yaschenko E. ? bmse000398 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID bmse000398 _Assembly.ID 1 _Assembly.Name 'Methylmalonic acid' _Assembly.Number_of_components 1 _Assembly.Organic_ligands 0 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state 'not reported' loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 Methylmalonic 1 $Methylmalonic yes native no no bmse000398 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_Methylmalonic _Entity.Sf_category entity _Entity.Sf_framecode Methylmalonic _Entity.Entry_ID bmse000398 _Entity.ID 1 _Entity.Name 'Methylmalonic acid' _Entity.Type non-polymer _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer no _Entity.Nstd_chirality no _Entity.Nstd_linkage no _Entity.Paramagnetic no _Entity.Thiol_state 'not reported' loop_ _Entity_comp_index.ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 1 $chem_comp_1 bmse000398 1 stop_ save_ #################### # Natural source # #################### save_natural_source _Entity_natural_src_list.Sf_category natural_source _Entity_natural_src_list.Sf_framecode natural_source _Entity_natural_src_list.Entry_ID bmse000398 _Entity_natural_src_list.ID 1 loop_ _Entity_natural_src.ID _Entity_natural_src.Entity_ID _Entity_natural_src.Entity_label _Entity_natural_src.NCBI_taxonomy_ID _Entity_natural_src.Type _Entity_natural_src.Common _Entity_natural_src.Organism_name_scientific _Entity_natural_src.Organism_name_common _Entity_natural_src.Superkingdom _Entity_natural_src.Kingdom _Entity_natural_src.Genus _Entity_natural_src.Species _Entity_natural_src.Entry_ID _Entity_natural_src.Entity_natural_src_list_ID 1 1 $Methylmalonic n/a 'multiple natural sources' yes 'not applicable' n/a n/a n/a n/a n/a bmse000398 1 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Entity_experimental_src_list.Sf_category experimental_source _Entity_experimental_src_list.Sf_framecode experimental_source _Entity_experimental_src_list.Entry_ID bmse000398 _Entity_experimental_src_list.ID 1 loop_ _Entity_experimental_src.ID _Entity_experimental_src.Entity_ID _Entity_experimental_src.Entity_label _Entity_experimental_src.Production_method _Entity_experimental_src.Entry_ID _Entity_experimental_src.Entity_experimental_src_list_ID 1 1 $Methylmalonic 'chemical synthesis' bmse000398 1 stop_ save_ ################################# # Polymer residues and ligands # ################################# save_chem_comp_1 _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_1 _Chem_comp.Entry_ID bmse000398 _Chem_comp.ID 1 _Chem_comp.Provenance PubChem _Chem_comp.Name 'Methylmalonic acid' _Chem_comp.Type non-polymer _Chem_comp.BMRB_code bmse000398 _Chem_comp.InChI_code InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8) _Chem_comp.Paramagnetic no _Chem_comp.Aromatic no _Chem_comp.Formula 'C4 H6 O4' _Chem_comp.Formula_weight 118.08804 _Chem_comp.Formula_mono_iso_wt_nat 118.026608681 _Chem_comp.Formula_mono_iso_wt_13C 122.0400280322 _Chem_comp.Formula_mono_iso_wt_15N 118.026608681 _Chem_comp.Formula_mono_iso_wt_13C_15N 122.0400280322 _Chem_comp.Image_file_name bmse000398.png _Chem_comp.Image_file_format png _Chem_comp.Struct_file_name bmse000398.mol _Chem_comp.Struct_file_format mol loop_ _Chem_comp_common_name.Name _Chem_comp_common_name.Type _Chem_comp_common_name.Entry_ID _Chem_comp_common_name.Comp_ID '2-methylpropanedioic acid' synonym bmse000398 1 methylmalonate synonym bmse000398 1 'methylmalonic acid' synonym bmse000398 1 '2-methylmalonic acid' synonym bmse000398 1 'Methylmalonic Acid' synonym bmse000398 1 '2-Methylpropanedioic acid' synonym bmse000398 1 '2-Methylmalonic acid' synonym bmse000398 1 'Propanedioic acid, methyl-' synonym bmse000398 1 Methylmalonate synonym bmse000398 1 MMA synonym bmse000398 1 'METHYL MALONIC ACID' synonym bmse000398 1 'Isosuccinic acid' synonym bmse000398 1 '1,1-Ethanedicarboxylic acid' synonym bmse000398 1 'propanedioic acid, methyl-' synonym bmse000398 1 'Methylmalonic acid' synonym bmse000398 1 'Propanedioic acid, methyl- (9CI)' synonym bmse000398 1 'Malonic acid, methyl-' synonym bmse000398 1 'methylpropanedioic acid' synonym bmse000398 1 stop_ loop_ _Chem_comp_descriptor.Descriptor _Chem_comp_descriptor.Type _Chem_comp_descriptor.Program _Chem_comp_descriptor.Program_version _Chem_comp_descriptor.Entry_ID _Chem_comp_descriptor.Comp_ID InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8) INCHI na na bmse000398 1 InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8) INCHI ALATIS 3.003 bmse000398 1 stop_ loop_ _Chem_comp_systematic_name.Name _Chem_comp_systematic_name.Naming_system _Chem_comp_systematic_name.Entry_ID _Chem_comp_systematic_name.Comp_ID '2-methylpropanedioic acid' PUBCHEM_IUPAC_NAME bmse000398 1 '2-methylmalonic acid' PUBCHEM_IUPAC_TRADITIONAL_NAME bmse000398 1 '2-methylpropanedioic acid' PUBCHEM_IUPAC_OPENEYE_NAME bmse000398 1 '2-methylpropanedioic acid' PUBCHEM_IUPAC_CAS_NAME bmse000398 1 '2-methylpropanedioic acid' PUBCHEM_IUPAC_SYSTEMATIC_NAME bmse000398 1 stop_ loop_ _Chem_comp_SMILES.Type _Chem_comp_SMILES.String _Chem_comp_SMILES.Entry_ID _Chem_comp_SMILES.Comp_ID canonical CC(C(=O)O)C(=O)O bmse000398 1 isomeric CC(C(=O)O)C(=O)O bmse000398 1 stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Drawing_2D_coord_x _Chem_comp_atom.Drawing_2D_coord_y _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Entry_ID _Chem_comp_atom.Comp_ID O5 O 6.0010 -0.2500 1 bmse000398 1 O7 O 2.5369 -0.2500 2 bmse000398 1 O6 O 5.1350 1.2500 3 bmse000398 1 O8 O 3.4030 1.2500 4 bmse000398 1 C2 C 4.2690 -0.2500 5 bmse000398 1 C1 C 4.2690 -1.2500 6 bmse000398 1 C3 C 5.1350 0.2500 7 bmse000398 1 C4 C 3.4030 0.2500 8 bmse000398 1 H12 H 4.8059 -0.5600 9 bmse000398 1 H9 H 3.6490 -1.2500 10 bmse000398 1 H11 H 4.2690 -1.8700 11 bmse000398 1 H10 H 4.8890 -1.2500 12 bmse000398 1 H13 H 6.5380 0.0600 13 bmse000398 1 H14 H 2.0000 0.0600 14 bmse000398 1 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID _Atom_nomenclature.Comp_ID O5 O1 BMRB bmse000398 1 O7 O2 BMRB bmse000398 1 O6 O3 BMRB bmse000398 1 O8 O4 BMRB bmse000398 1 C2 C5 BMRB bmse000398 1 C1 C6 BMRB bmse000398 1 C3 C7 BMRB bmse000398 1 C4 C8 BMRB bmse000398 1 H12 H9 BMRB bmse000398 1 H9 H10 BMRB bmse000398 1 H11 H11 BMRB bmse000398 1 H10 H12 BMRB bmse000398 1 H13 H13 BMRB bmse000398 1 H14 H14 BMRB bmse000398 1 O5 O5 ALATIS bmse000398 1 O7 O7 ALATIS bmse000398 1 O6 O6 ALATIS bmse000398 1 O8 O8 ALATIS bmse000398 1 C2 C2 ALATIS bmse000398 1 C1 C1 ALATIS bmse000398 1 C3 C3 ALATIS bmse000398 1 C4 C4 ALATIS bmse000398 1 H12 H12 ALATIS bmse000398 1 H9 H9 ALATIS bmse000398 1 H11 H11 ALATIS bmse000398 1 H10 H10 ALATIS bmse000398 1 H13 H13 ALATIS bmse000398 1 H14 H14 ALATIS bmse000398 1 stop_ loop_ _Chem_comp_bond.ID _Chem_comp_bond.Type _Chem_comp_bond.Value_order _Chem_comp_bond.Atom_ID_1 _Chem_comp_bond.Atom_ID_2 _Chem_comp_bond.Entry_ID _Chem_comp_bond.Comp_ID 1 covalent SING O5 C3 bmse000398 1 2 covalent SING O5 H13 bmse000398 1 3 covalent SING O7 C4 bmse000398 1 4 covalent SING O7 H14 bmse000398 1 5 covalent DOUB O6 C3 bmse000398 1 6 covalent DOUB O8 C4 bmse000398 1 7 covalent SING C2 C1 bmse000398 1 8 covalent SING C2 C3 bmse000398 1 9 covalent SING C2 C4 bmse000398 1 10 covalent SING C2 H12 bmse000398 1 11 covalent SING C1 H9 bmse000398 1 12 covalent SING C1 H11 bmse000398 1 13 covalent SING C1 H10 bmse000398 1 stop_ loop_ _Chem_comp_db_link.Author_supplied _Chem_comp_db_link.Database_code _Chem_comp_db_link.Accession_code _Chem_comp_db_link.Accession_code_type _Chem_comp_db_link.Entry_mol_name _Chem_comp_db_link.Entry_relation_type _Chem_comp_db_link.Entry_ID _Chem_comp_db_link.Comp_ID no PubChem 85165190 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 487 cid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 5992023 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 8145370 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 587340 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 46506625 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 24896996 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 5245 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 37915082 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 10524907 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 153879 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no PubChem 2437 sid 'Methylmalonic acid' 'matching entry' bmse000398 1 no 'CAS Registry' 516-05-2 'registry number' 'Methylmalonic acid' 'matching entry' bmse000398 1 no Sigma-Aldrich M54058_ALDRICH ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no ChEBI CHEBI:30860 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no BioCyc CPD-546 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no ChemIDplus 000516052 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no ChemSpider 13886495 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no DrugBank DB04183 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no EINECS 208-219-5 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no KEGG C02170 'compound ID' 'Methylmalonic acid' 'matching entry' bmse000398 1 no NMRShiftDB 19792 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no 'Beilstein Handbook Reference' 4-02-00-01932 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no ChemDB 6688378 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no 'NIST Chemistry WebBook' 3181377847 ? 'Methylmalonic acid' 'matching entry' bmse000398 1 no PDB DXX 'Chemical Component' 'Methylmalonic acid' 'matching entry' bmse000398 1 stop_ loop_ _Chem_comp_citation.Citation_ID _Chem_comp_citation.Citation_label _Chem_comp_citation.Entry_ID _Chem_comp_citation.Comp_ID 1 $citation_1 bmse000398 1 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID bmse000398 _Sample.ID 1 _Sample.Type solution loop_ _Sample_component.ID _Sample_component.Mol_common_name _Sample_component.Isotopic_labeling _Sample_component.Entity_ID _Sample_component.Entity_label _Sample_component.Type _Sample_component.Concentration_val _Sample_component.Concentration_val_units _Sample_component.Vendor _Sample_component.Vendor_product_name _Sample_component.Vendor_product_code _Sample_component.Entry_ID _Sample_component.Sample_ID 1 'Methylmalonic acid' 'natural abundance' 1 $Methylmalonic Solute 100 mM Aldrich 'Methylmalonic acid' 03021MD bmse000398 1 2 D2O ? 1 ? Solvent 100 % ? ? ? bmse000398 1 3 'sodium phosphate' ? 1 ? Buffer 50 mM ? ? ? bmse000398 1 4 'sodium azide' ? 1 ? Cytocide 500 uM ? ? ? bmse000398 1 5 DSS ? 1 ? Reference 500 uM ? ? ? bmse000398 1 stop_ save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Sample_condition_list.Sf_category sample_conditions _Sample_condition_list.Sf_framecode sample_conditions_1 _Sample_condition_list.Entry_ID bmse000398 _Sample_condition_list.ID 1 loop_ _Sample_condition_variable.Type _Sample_condition_variable.Val _Sample_condition_variable.Val_units _Sample_condition_variable.Entry_ID _Sample_condition_variable.Sample_condition_list_ID pH 7.4 pH bmse000398 1 temperature 298 K bmse000398 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmse000398 _Software.ID 1 _Software.Name NMRPipe loop_ _Vendor.Name _Vendor.Entry_ID _Vendor.Software_ID 'F Delaglio, S Grzesiek, GW Vuister, G Zhu, J Pfeifer and A Bax' bmse000398 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID Processing bmse000398 1 stop_ save_ save_software_2 _Software.Sf_category software _Software.Sf_framecode software_2 _Software.Entry_ID bmse000398 _Software.ID 2 _Software.Name XWIN-NMR _Software.Version 3.5 loop_ _Vendor.Name _Vendor.Entry_ID _Vendor.Software_ID 'Bruker Biospin' bmse000398 2 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID Collection bmse000398 2 Processing bmse000398 2 'Data analysis' bmse000398 2 'Peak picking' bmse000398 2 stop_ save_ save_software_3 _Software.Sf_category software _Software.Sf_framecode software_3 _Software.Entry_ID bmse000398 _Software.ID 3 _Software.Name NMRDraw _Software.Version 2.3 loop_ _Vendor.Name _Vendor.Entry_ID _Vendor.Software_ID 'F Delaglio, S Grzesiek, GW Vuister, G Zhu, J Pfeifer and A Bax' bmse000398 3 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'Data analysis' bmse000398 3 'Peak picking' bmse000398 3 stop_ save_ save_software_4 _Software.Sf_category software _Software.Sf_framecode software_4 _Software.Entry_ID bmse000398 _Software.ID 4 _Software.Name NUTS _Software.Version '1D Version - 20060331' loop_ _Vendor.Name _Vendor.Entry_ID _Vendor.Software_ID 'Acorn NMR Inc.' bmse000398 4 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'Data analysis' bmse000398 4 'Peak picking' bmse000398 4 stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker_DMX_500 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode Bruker_DMX_500 _NMR_spectrometer.Entry_ID bmse000398 _NMR_spectrometer.ID 1 _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model DMX _NMR_spectrometer.Field_strength 500 save_ ############################# # NMR applied experiments # ############################# save_experiment_list _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list _Experiment_list.Entry_ID bmse000398 _Experiment_list.ID 1 loop_ _Experiment.ID _Experiment.Name _Experiment.Raw_data_flag _Experiment.Sample_ID _Experiment.Sample_label _Experiment.Sample_state _Experiment.Sample_condition_list_ID _Experiment.Sample_condition_list_label _Experiment.NMR_spectrometer_ID _Experiment.NMR_spectrometer_label _Experiment.Entry_ID _Experiment.Experiment_list_ID 1 '1D 1H' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000398 1 2 '2D [1H,1H]-TOCSY' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000398 1 3 '1D 13C' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000398 1 4 '1D DEPT90' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000398 1 5 '1D DEPT135' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000398 1 6 '2D [1H,13C]-HSQC' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000398 1 7 '2D [1H,13C]-HMBC' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000398 1 stop_ loop_ _Experiment_file.Experiment_ID _Experiment_file.Name _Experiment_file.Type _Experiment_file.Directory_path _Experiment_file.Details _Experiment_file.Entry_ID _Experiment_file.Experiment_list_ID 1 1 text/directory nmr/set01/ 'NMR experiment directory' bmse000398 1 1 1H.png image/png nmr/set01/spectra 'Spectral image' bmse000398 1 2 2 text/directory nmr/set01/ 'NMR experiment directory' bmse000398 1 2 HH_TOCSY.png image/png nmr/set01/spectra 'Spectral image' bmse000398 1 3 3 text/directory nmr/set01/ 'NMR experiment directory' bmse000398 1 3 13C.png image/png nmr/set01/spectra 'Spectral image' bmse000398 1 4 4 text/directory nmr/set01/ 'NMR experiment directory' bmse000398 1 4 DEPT_90.png image/png nmr/set01/spectra 'Spectral image' bmse000398 1 5 5 text/directory nmr/set01/ 'NMR experiment directory' bmse000398 1 5 DEPT_135.png image/png nmr/set01/spectra 'Spectral image' bmse000398 1 6 6 text/directory nmr/set01/ 'NMR experiment directory' bmse000398 1 6 1H_13C_HSQC.png image/png nmr/set01/spectra 'Spectral image' bmse000398 1 7 7 text/directory nmr/set01/ 'NMR experiment directory' bmse000398 1 7 1H_13C_HMBC.png image/png nmr/set01/spectra 'Spectral image' bmse000398 1 stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference _Chem_shift_reference.Sf_category chem_shift_reference _Chem_shift_reference.Sf_framecode chem_shift_reference _Chem_shift_reference.Entry_ID bmse000398 _Chem_shift_reference.ID 1 loop_ _Chem_shift_ref.Atom_type _Chem_shift_ref.Atom_isotope_number _Chem_shift_ref.Mol_common_name _Chem_shift_ref.Atom_group _Chem_shift_ref.Chem_shift_units _Chem_shift_ref.Chem_shift_val _Chem_shift_ref.Ref_method _Chem_shift_ref.Ref_type _Chem_shift_ref.Indirect_shift_ratio _Chem_shift_ref.Entry_ID _Chem_shift_ref.Chem_shift_reference_ID H 1 DSS 'methyl protons' ppm 0.00 internal direct 1.000000000 bmse000398 1 C 13 DSS 'methyl protons' ppm 0.00 ? indirect 0.251449530 bmse000398 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts _Assigned_chem_shift_list.Sf_category assigned_chemical_shifts _Assigned_chem_shift_list.Sf_framecode assigned_chemical_shifts _Assigned_chem_shift_list.Entry_ID bmse000398 _Assigned_chem_shift_list.ID 1 _Assigned_chem_shift_list.Sample_condition_list_ID 1 _Assigned_chem_shift_list.Sample_condition_list_label $sample_conditions_1 _Assigned_chem_shift_list.Chem_shift_reference_ID 1 _Assigned_chem_shift_list.Chem_shift_reference_label $chem_shift_reference loop_ _Chem_shift_experiment.Experiment_ID _Chem_shift_experiment.Experiment_name _Chem_shift_experiment.Sample_ID _Chem_shift_experiment.Sample_label _Chem_shift_experiment.Entry_ID _Chem_shift_experiment.Assigned_chem_shift_list_ID 1 '1D 1H' 1 $sample_1 bmse000398 1 2 '2D [1H,1H]-TOCSY' 1 $sample_1 bmse000398 1 3 '1D 13C' 1 $sample_1 bmse000398 1 4 '1D DEPT90' 1 $sample_1 bmse000398 1 5 '1D DEPT135' 1 $sample_1 bmse000398 1 6 '2D [1H,13C]-HSQC' 1 $sample_1 bmse000398 1 7 '2D [1H,13C]-HMBC' 1 $sample_1 bmse000398 1 stop_ loop_ _Chem_shift_software.Software_ID _Chem_shift_software.Software_label _Chem_shift_software.Entry_ID _Chem_shift_software.Assigned_chem_shift_list_ID 1 $software_2 bmse000398 1 stop_ loop_ _Atom_chem_shift.ID _Atom_chem_shift.Entity_ID _Atom_chem_shift.Comp_index_ID _Atom_chem_shift.Comp_ID _Atom_chem_shift.Atom_ID _Atom_chem_shift.Atom_type _Atom_chem_shift.Atom_isotope_number _Atom_chem_shift.Val _Atom_chem_shift.Ambiguity_code _Atom_chem_shift.Auth_atom_ID _Atom_chem_shift.Entry_ID _Atom_chem_shift.Assigned_chem_shift_list_ID 1 1 1 1 C2 C 13 54.478 1 C5 bmse000398 1 2 1 1 1 C1 C 13 17.837 1 C6 bmse000398 1 3 1 1 1 C3 C 13 183.723 1 C7 bmse000398 1 4 1 1 1 C4 C 13 183.723 1 C8 bmse000398 1 5 1 1 1 H12 H 1 3.154 1 H9 bmse000398 1 6 1 1 1 H9 H 1 1.217 1 H10 bmse000398 1 7 1 1 1 H11 H 1 1.217 1 H11 bmse000398 1 8 1 1 1 H10 H 1 1.217 1 H12 bmse000398 1 stop_ save_ ######################### # Spectral peak lists # ######################### save_spectral_peak_1H _Spectral_peak_list.Sf_category spectral_peak_list _Spectral_peak_list.Sf_framecode spectral_peak_1H _Spectral_peak_list.Entry_ID bmse000398 _Spectral_peak_list.ID 1 _Spectral_peak_list.Sample_ID 1 _Spectral_peak_list.Sample_label $sample_1 _Spectral_peak_list.Sample_condition_list_ID 1 _Spectral_peak_list.Sample_condition_list_label $sample_conditions_1 _Spectral_peak_list.Experiment_ID 1 _Spectral_peak_list.Experiment_name '1D 1H' _Spectral_peak_list.Number_of_spectral_dimensions 1 loop_ _Spectral_dim.ID _Spectral_dim.Atom_type _Spectral_dim.Atom_isotope_number _Spectral_dim.Spectral_region _Spectral_dim.Sweep_width _Spectral_dim.Entry_ID _Spectral_dim.Spectral_peak_list_ID 1 H 1 'Full H' 7002.80112044818 bmse000398 1 stop_ loop_ _Spectral_peak_software.Software_ID _Spectral_peak_software.Software_label _Spectral_peak_software.Entry_ID _Spectral_peak_software.Spectral_peak_list_ID 2 $software_2 bmse000398 1 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse000398 1 2 bmse000398 1 stop_ loop_ _Peak_general_char.Peak_ID _Peak_general_char.Intensity_val _Peak_general_char.Measurement_method _Peak_general_char.Entry_ID _Peak_general_char.Spectral_peak_list_ID 1 3 integration bmse000398 1 2 0.05 integration bmse000398 1 stop_ loop_ _Peak_char.Peak_ID _Peak_char.Spectral_dim_ID _Peak_char.Chem_shift_val _Peak_char.Coupling_pattern _Peak_char.Entry_ID _Peak_char.Spectral_peak_list_ID 1 1 1.217 s bmse000398 1 2 1 3.154 q bmse000398 1 stop_ loop_ _Assigned_peak_chem_shift.Peak_ID _Assigned_peak_chem_shift.Spectral_dim_ID _Assigned_peak_chem_shift.Val _Assigned_peak_chem_shift.Entity_ID _Assigned_peak_chem_shift.Comp_index_ID _Assigned_peak_chem_shift.Comp_ID _Assigned_peak_chem_shift.Atom_ID _Assigned_peak_chem_shift.Entry_ID _Assigned_peak_chem_shift.Spectral_peak_list_ID 1 1 1.217 1 1 1 H9 bmse000398 1 1 1 1.217 1 1 1 H11 bmse000398 1 1 1 1.217 1 1 1 H10 bmse000398 1 2 1 3.154 1 1 1 H12 bmse000398 1 stop_ loop_ _Spectral_transition.ID _Spectral_transition.Entry_ID _Spectral_transition.Spectral_peak_list_ID 1 bmse000398 1 stop_ loop_ _Spectral_transition_general_char.Spectral_transition_ID _Spectral_transition_general_char.Intensity_val _Spectral_transition_general_char.Measurement_method _Spectral_transition_general_char.Entry_ID _Spectral_transition_general_char.Spectral_peak_list_ID 1 100.174 Height bmse000398 1 stop_ loop_ _Spectral_transition_char.Spectral_transition_ID _Spectral_transition_char.Spectral_dim_ID _Spectral_transition_char.Chem_shift_val _Spectral_transition_char.Entry_ID _Spectral_transition_char.Spectral_peak_list_ID 1 1 1.217 bmse000398 1 stop_ save_ save_spectral_peak_13C _Spectral_peak_list.Sf_category spectral_peak_list _Spectral_peak_list.Sf_framecode spectral_peak_13C _Spectral_peak_list.Entry_ID bmse000398 _Spectral_peak_list.ID 2 _Spectral_peak_list.Sample_ID 1 _Spectral_peak_list.Sample_label $sample_1 _Spectral_peak_list.Sample_condition_list_ID 1 _Spectral_peak_list.Sample_condition_list_label $sample_conditions_1 _Spectral_peak_list.Experiment_ID 3 _Spectral_peak_list.Experiment_name '1D 13C' _Spectral_peak_list.Number_of_spectral_dimensions 1 loop_ _Spectral_dim.ID _Spectral_dim.Atom_type _Spectral_dim.Atom_isotope_number _Spectral_dim.Spectral_region _Spectral_dim.Sweep_width _Spectral_dim.Entry_ID _Spectral_dim.Spectral_peak_list_ID 1 C 13 'Full C' 27777.7777777778 bmse000398 2 stop_ loop_ _Spectral_peak_software.Software_ID _Spectral_peak_software.Software_label _Spectral_peak_software.Entry_ID _Spectral_peak_software.Spectral_peak_list_ID 2 $software_2 bmse000398 2 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse000398 2 2 bmse000398 2 3 bmse000398 2 stop_ loop_ _Peak_char.Peak_ID _Peak_char.Spectral_dim_ID _Peak_char.Chem_shift_val _Peak_char.Coupling_pattern _Peak_char.Entry_ID _Peak_char.Spectral_peak_list_ID 1 1 183.723 s bmse000398 2 2 1 54.478 s bmse000398 2 3 1 17.837 s bmse000398 2 stop_ loop_ _Assigned_peak_chem_shift.Peak_ID _Assigned_peak_chem_shift.Spectral_dim_ID _Assigned_peak_chem_shift.Val _Assigned_peak_chem_shift.Entity_ID _Assigned_peak_chem_shift.Comp_index_ID _Assigned_peak_chem_shift.Comp_ID _Assigned_peak_chem_shift.Atom_ID _Assigned_peak_chem_shift.Entry_ID _Assigned_peak_chem_shift.Spectral_peak_list_ID 1 1 183.723 1 1 1 C3 bmse000398 2 1 1 183.723 1 1 1 C4 bmse000398 2 2 1 54.478 1 1 1 C2 bmse000398 2 3 1 17.837 1 1 1 C1 bmse000398 2 stop_ loop_ _Spectral_transition.ID _Spectral_transition.Entry_ID _Spectral_transition.Spectral_peak_list_ID 1 bmse000398 2 2 bmse000398 2 3 bmse000398 2 stop_ loop_ _Spectral_transition_general_char.Spectral_transition_ID _Spectral_transition_general_char.Intensity_val _Spectral_transition_general_char.Measurement_method _Spectral_transition_general_char.Entry_ID _Spectral_transition_general_char.Spectral_peak_list_ID 1 40.033 Height bmse000398 2 2 9.414 Height bmse000398 2 3 99.485 Height bmse000398 2 stop_ loop_ _Spectral_transition_char.Spectral_transition_ID _Spectral_transition_char.Spectral_dim_ID _Spectral_transition_char.Chem_shift_val _Spectral_transition_char.Entry_ID _Spectral_transition_char.Spectral_peak_list_ID 1 1 183.733 bmse000398 2 2 1 54.497 bmse000398 2 3 1 17.859 bmse000398 2 stop_ save_ save_spectral_peak_DEPT_135 _Spectral_peak_list.Sf_category spectral_peak_list _Spectral_peak_list.Sf_framecode spectral_peak_DEPT_135 _Spectral_peak_list.Entry_ID bmse000398 _Spectral_peak_list.ID 3 _Spectral_peak_list.Sample_ID 1 _Spectral_peak_list.Sample_label $sample_1 _Spectral_peak_list.Sample_condition_list_ID 1 _Spectral_peak_list.Sample_condition_list_label $sample_conditions_1 _Spectral_peak_list.Experiment_ID 5 _Spectral_peak_list.Experiment_name '1D DEPT135' _Spectral_peak_list.Number_of_spectral_dimensions 1 loop_ _Spectral_dim.ID _Spectral_dim.Atom_type _Spectral_dim.Atom_isotope_number _Spectral_dim.Spectral_region _Spectral_dim.Sweep_width _Spectral_dim.Entry_ID _Spectral_dim.Spectral_peak_list_ID 1 C 13 'Full C' 27662.5172890733 bmse000398 3 stop_ loop_ _Spectral_peak_software.Software_ID _Spectral_peak_software.Software_label _Spectral_peak_software.Entry_ID _Spectral_peak_software.Spectral_peak_list_ID 2 $software_2 bmse000398 3 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse000398 3 stop_ loop_ _Peak_char.Peak_ID _Peak_char.Spectral_dim_ID _Peak_char.Chem_shift_val _Peak_char.Phase_val _Peak_char.Coupling_pattern _Peak_char.Entry_ID _Peak_char.Spectral_peak_list_ID 1 1 17.827 positive s bmse000398 3 stop_ loop_ _Assigned_peak_chem_shift.Peak_ID _Assigned_peak_chem_shift.Spectral_dim_ID _Assigned_peak_chem_shift.Val _Assigned_peak_chem_shift.Entity_ID _Assigned_peak_chem_shift.Comp_index_ID _Assigned_peak_chem_shift.Comp_ID _Assigned_peak_chem_shift.Atom_ID _Assigned_peak_chem_shift.Entry_ID _Assigned_peak_chem_shift.Spectral_peak_list_ID 1 1 17.827 1 1 1 C1 bmse000398 3 stop_ save_ save_spectral_peak_1H_13C_HSQC _Spectral_peak_list.Sf_category spectral_peak_list _Spectral_peak_list.Sf_framecode spectral_peak_1H_13C_HSQC _Spectral_peak_list.Entry_ID bmse000398 _Spectral_peak_list.ID 4 _Spectral_peak_list.Sample_ID 1 _Spectral_peak_list.Sample_label $sample_1 _Spectral_peak_list.Sample_condition_list_ID 1 _Spectral_peak_list.Sample_condition_list_label $sample_conditions_1 _Spectral_peak_list.Experiment_ID 6 _Spectral_peak_list.Experiment_name '2D [1H,13C]-HSQC' _Spectral_peak_list.Number_of_spectral_dimensions 2 loop_ _Spectral_dim.ID _Spectral_dim.Atom_type _Spectral_dim.Atom_isotope_number _Spectral_dim.Spectral_region _Spectral_dim.Sweep_width _Spectral_dim.Entry_ID _Spectral_dim.Spectral_peak_list_ID 1 H 1 'Full H' 7002.80112044818 bmse000398 4 2 C 13 'Full C' 22434.0998317442 bmse000398 4 stop_ loop_ _Spectral_peak_software.Software_ID _Spectral_peak_software.Software_label _Spectral_peak_software.Entry_ID _Spectral_peak_software.Spectral_peak_list_ID 1 $software_1 bmse000398 4 3 $software_3 bmse000398 4 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse000398 4 stop_ loop_ _Peak_char.Peak_ID _Peak_char.Spectral_dim_ID _Peak_char.Chem_shift_val _Peak_char.Entry_ID _Peak_char.Spectral_peak_list_ID 1 1 1.241 bmse000398 4 1 2 17.617 bmse000398 4 stop_ loop_ _Assigned_peak_chem_shift.Peak_ID _Assigned_peak_chem_shift.Spectral_dim_ID _Assigned_peak_chem_shift.Val _Assigned_peak_chem_shift.Entity_ID _Assigned_peak_chem_shift.Comp_index_ID _Assigned_peak_chem_shift.Comp_ID _Assigned_peak_chem_shift.Atom_ID _Assigned_peak_chem_shift.Entry_ID _Assigned_peak_chem_shift.Spectral_peak_list_ID 1 1 1.241 1 1 1 H9 bmse000398 4 1 1 1.241 1 1 1 H11 bmse000398 4 1 1 1.241 1 1 1 H10 bmse000398 4 1 2 17.617 1 1 1 C1 bmse000398 4 stop_ save_ save_spectral_peak_1H_13C_HMBC _Spectral_peak_list.Sf_category spectral_peak_list _Spectral_peak_list.Sf_framecode spectral_peak_1H_13C_HMBC _Spectral_peak_list.Entry_ID bmse000398 _Spectral_peak_list.ID 5 _Spectral_peak_list.Sample_ID 1 _Spectral_peak_list.Sample_label $sample_1 _Spectral_peak_list.Sample_condition_list_ID 1 _Spectral_peak_list.Sample_condition_list_label $sample_conditions_1 _Spectral_peak_list.Experiment_ID 7 _Spectral_peak_list.Experiment_name '2D [1H,13C]-HMBC' _Spectral_peak_list.Number_of_spectral_dimensions 2 loop_ _Spectral_dim.ID _Spectral_dim.Atom_type _Spectral_dim.Atom_isotope_number _Spectral_dim.Spectral_region _Spectral_dim.Sweep_width _Spectral_dim.Entry_ID _Spectral_dim.Spectral_peak_list_ID 1 H 1 'Full H' 6510.41666666667 bmse000398 5 2 C 13 'Full C' 27662.5172890733 bmse000398 5 stop_ loop_ _Spectral_peak_software.Software_ID _Spectral_peak_software.Software_label _Spectral_peak_software.Entry_ID _Spectral_peak_software.Spectral_peak_list_ID 1 $software_1 bmse000398 5 3 $software_3 bmse000398 5 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse000398 5 2 bmse000398 5 stop_ loop_ _Peak_char.Peak_ID _Peak_char.Spectral_dim_ID _Peak_char.Chem_shift_val _Peak_char.Entry_ID _Peak_char.Spectral_peak_list_ID 1 1 1.123 bmse000398 5 1 2 54.886 bmse000398 5 2 1 3.066 bmse000398 5 2 2 183.389 bmse000398 5 stop_ loop_ _Assigned_peak_chem_shift.Peak_ID _Assigned_peak_chem_shift.Spectral_dim_ID _Assigned_peak_chem_shift.Val _Assigned_peak_chem_shift.Entity_ID _Assigned_peak_chem_shift.Comp_index_ID _Assigned_peak_chem_shift.Comp_ID _Assigned_peak_chem_shift.Atom_ID _Assigned_peak_chem_shift.Entry_ID _Assigned_peak_chem_shift.Spectral_peak_list_ID 1 1 1.123 1 1 1 H9 bmse000398 5 1 1 1.123 1 1 1 H11 bmse000398 5 1 1 1.123 1 1 1 H10 bmse000398 5 1 2 54.886 1 1 1 C1 bmse000398 5 2 1 3.066 1 1 1 H12 bmse000398 5 2 2 183.389 1 1 1 C3 bmse000398 5 2 2 183.389 1 1 1 C4 bmse000398 5 stop_ save_