data_6659 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 15N hyperfine shifts assignment for wild-type rubredoxin from Clostridium pasteurianum in the oxidized state ; _BMRB_accession_number 6659 _BMRB_flat_file_name bmr6659.str _Entry_type original _Submission_date 2005-06-08 _Accession_date 2005-06-08 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lin I-Jin . . 2 Gebel Erika B. . 3 Machonkin Timothy E. . 4 Westler William M. . 5 Markley John L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "15N chemical shifts" 12 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2005-12-14 original author . stop_ _Original_release_date 2005-12-14 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Changes in hydrogen-bond strengths explain reduction potentials in 10 rubredoxin variants. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lin I-Jin . . 2 Gebel Erika . . 3 Machonkin Timothy . . 4 Westler William . . 5 Markley John L. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U. S. A.' _Journal_volume 11 _Journal_issue 102 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 14581 _Page_last 14586 _Year 2005 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name rubredoxin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label rubredoxin $rubredoxin 'FE (III) ION' $FE stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic yes _System_thiol_state 'all other bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_rubredoxin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common rubredoxin _Molecular_mass . _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 54 _Mol_residue_sequence ; MKKYTCTVCGYIYNPEDGDP DNGVNPGTDFKDIPDDWVCP LCGVGKDQFEEVEE ; loop_ _Residue_seq_code _Residue_label 1 MET 2 LYS 3 LYS 4 TYR 5 THR 6 CYS 7 THR 8 VAL 9 CYS 10 GLY 11 TYR 12 ILE 13 TYR 14 ASN 15 PRO 16 GLU 17 ASP 18 GLY 19 ASP 20 PRO 21 ASP 22 ASN 23 GLY 24 VAL 25 ASN 26 PRO 27 GLY 28 THR 29 ASP 30 PHE 31 LYS 32 ASP 33 ILE 34 PRO 35 ASP 36 ASP 37 TRP 38 VAL 39 CYS 40 PRO 41 LEU 42 CYS 43 GLY 44 VAL 45 GLY 46 LYS 47 ASP 48 GLN 49 PHE 50 GLU 51 GLU 52 VAL 53 GLU 54 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-21 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 4050 Rdx 100.00 54 100.00 100.00 3.18e-30 BMRB 4051 Rdx 100.00 54 100.00 100.00 3.18e-30 BMRB 4066 RdxIII 100.00 54 100.00 100.00 3.18e-30 BMRB 4137 RdxII 100.00 54 100.00 100.00 3.18e-30 BMRB 4182 cprd 100.00 54 100.00 100.00 3.18e-30 BMRB 4319 Rdx 100.00 54 100.00 100.00 3.18e-30 BMRB 4320 Rdx 100.00 54 100.00 100.00 3.18e-30 BMRB 5600 MetCpRdZn 100.00 54 100.00 100.00 3.18e-30 BMRB 6660 rubredoxin 100.00 54 98.15 98.15 7.74e-30 BMRB 6661 rubredoxin 100.00 54 98.15 98.15 7.74e-30 BMRB 6662 rubredoxin 100.00 54 98.15 98.15 7.74e-30 BMRB 6663 rubredoxin 100.00 54 98.15 98.15 7.74e-30 BMRB 6664 rubredoxin 100.00 54 98.15 98.15 7.74e-30 BMRB 6667 rubredoxin 100.00 54 98.15 100.00 4.40e-30 BMRB 6668 rubredoxin 100.00 54 98.15 100.00 4.40e-30 BMRB 6669 rubredoxin 100.00 54 98.15 100.00 6.37e-30 BMRB 6670 rubredoxin 100.00 54 98.15 100.00 6.37e-30 BMRB 6673 rubredoxin 100.00 54 98.15 98.15 4.03e-29 BMRB 6674 rubredoxin 100.00 54 98.15 98.15 4.03e-29 BMRB 6675 rubredoxin 100.00 54 98.15 100.00 4.40e-30 BMRB 6676 rubredoxin 100.00 54 98.15 100.00 4.40e-30 BMRB 6677 rubredoxin 100.00 54 98.15 100.00 6.37e-30 BMRB 6678 rubredoxin 100.00 54 98.15 100.00 6.37e-30 PDB 1B13 "Clostridium Pasteurianum Rubredoxin G10a Mutant" 100.00 54 98.15 98.15 9.62e-30 PDB 1B2J "Clostridium Pasteurianum Rubredoxin G43a Mutant" 100.00 54 98.15 98.15 9.62e-30 PDB 1BE7 "Clostridium Pasteurianum Rubredoxin C42s Mutant" 100.00 54 98.15 98.15 2.34e-29 PDB 1BFY "Solution Structure Of Reduced Clostridium Pasteurianum Rubredoxin, Nmr, 20 Structures" 98.15 54 100.00 100.00 3.42e-29 PDB 1C09 "Rubredoxin V44a Cp" 100.00 54 98.15 98.15 7.74e-30 PDB 1FHH "X-Ray Crystal Structure Of Oxidized Rubredoxin" 100.00 54 100.00 100.00 3.18e-30 PDB 1FHM "X-Ray Crystal Structure Of Reduced Rubredoxin" 100.00 54 100.00 100.00 3.18e-30 PDB 1IRN "Rubredoxin (zn-substituted) At 1.2 Angstroms Resolution" 100.00 54 100.00 100.00 3.18e-30 PDB 1IRO "Rubredoxin (Oxidized, Fe(Iii)) At 1.1 Angstroms Resolution" 100.00 54 100.00 100.00 3.18e-30 PDB 1R0F "Gallium-Substituted Rubredoxin" 100.00 54 100.00 100.00 3.18e-30 PDB 1R0G "Mercury-Substituted Rubredoxin" 100.00 54 100.00 100.00 3.18e-30 PDB 1R0H "Cobalt-Substituted Rubredoxin" 100.00 54 100.00 100.00 3.18e-30 PDB 1R0I "Cadmium-Substituted Rubredoxin" 100.00 54 100.00 100.00 3.18e-30 PDB 1R0J "Nickel-Substituted Rubredoxin" 100.00 54 100.00 100.00 3.18e-30 PDB 1SMM "Crystal Structure Of Cp Rd L41a Mutant In Oxidized State" 100.00 54 98.15 98.15 1.62e-29 PDB 1SMU "Crystal Structure Of Cp Rd L41a Mutant In Reduced State 1 (Drop-Reduced)" 100.00 54 98.15 98.15 1.62e-29 PDB 1SMW "Crystal Structure Of Cp Rd L41a Mutant In Reduced State 2 (Soaked)" 100.00 54 98.15 98.15 1.62e-29 PDB 1T9O "Crystal Structure Of V44g Cp Rubredoxin" 100.00 54 98.15 98.15 4.03e-29 PDB 1T9Q "Crystal Structure Of V44l Cp Rubredoxin" 100.00 54 98.15 100.00 6.37e-30 PDB 4MBS "Crystal Structure Of The Ccr5 Chemokine Receptor" 100.00 414 100.00 100.00 1.66e-35 GB AAA23279 "rubredoxin [Clostridium pasteurianum]" 100.00 54 100.00 100.00 3.18e-30 GB AJA49845 "rubredoxin [Clostridium pasteurianum DSM 525 = ATCC 6013]" 100.00 54 100.00 100.00 3.18e-30 GB AJA53833 "rubredoxin [Clostridium pasteurianum DSM 525 = ATCC 6013]" 100.00 54 100.00 100.00 3.18e-30 GB ELP57804 "Rubredoxin [Clostridium pasteurianum DSM 525 = ATCC 6013]" 100.00 54 100.00 100.00 3.18e-30 GB KER11884 "Rubredoxin domain containing protein [Clostridium pasteurianum DSM 525 = ATCC 6013]" 100.00 54 100.00 100.00 3.18e-30 REF WP_003447684 "Rubredoxin [Clostridium pasteurianum]" 100.00 54 100.00 100.00 3.18e-30 SP P00268 "RecName: Full=Rubredoxin; Short=Rd [Clostridium pasteurianum]" 100.00 54 100.00 100.00 3.18e-30 stop_ save_ ############# # Ligands # ############# save_FE _Saveframe_category ligand _Mol_type non-polymer _Name_common "FE (FE (III) ION)" _BMRB_code . _PDB_code FE _Molecular_mass 55.845 _Mol_charge 3 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 8 14:33:55 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons FE FE FE . 3 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $rubredoxin 'Clostridium pasteurianum' 1501 Bacteria . Clostridium pasteurianum stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $rubredoxin 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_Wild-type_oxidized_rubredoxin _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $rubredoxin . mM . 'phospate buffer' 50 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_500MHz_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model . _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_1D_15N_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 15N' _Sample_label $Wild-type_oxidized_rubredoxin save_ save_1D_15N _Saveframe_category NMR_applied_experiment _Experiment_name '1D 15N' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_50mM_phospate_buffer _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6 . pH temperature 293 0.2 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_referencing _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0 internal indirect . . . 1.0 $entry_citation $entry_citation DSS N 15 'methyl protons' ppm 0.0 . indirect . . . 0.101329118 $entry_citation $entry_citation 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $Wild-type_oxidized_rubredoxin stop_ _Sample_conditions_label $50mM_phospate_buffer _Chem_shift_reference_set_label $chemical_shift_referencing _Mol_system_component_name rubredoxin _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 6 6 CYS N N 613 0.5 2 2 7 7 THR N N 358 0.5 1 3 8 8 VAL N N 525 0.5 1 4 9 9 CYS N N -34 0.5 1 5 10 10 GLY N N 311 0.5 1 6 11 11 TYR N N 633 0.5 1 7 39 39 CYS N N 588 0.5 2 8 40 40 PRO N N 407 0.5 1 9 41 41 LEU N N 542 0.5 1 10 42 42 CYS N N -79 0.5 1 11 43 43 GLY N N 327 0.5 1 12 44 44 VAL N N 346 0.5 1 stop_ save_