data_50186 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Identification of a novel N-linked glycan on the Archaellins and S-layer protein of the thermophilic methanogen, Methanothermococcus thermolithotrophicus ; _BMRB_accession_number 50186 _BMRB_flat_file_name bmr50186.str _Entry_type original _Submission_date 2020-01-30 _Accession_date 2020-01-30 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; Identification of a Novel Glycan N-linked to the Archaellins and S-layer protein of the thermophilic methanogen, Methanothermococcus thermolithotrophicus. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kelly John F. . 2 Vinogradov Evguenii . . 3 Stupak Jacek . . 4 Robotham Anna C. . 5 Logan Susan M. . 6 Berezuk Alison . . 7 Khursigara Cezar M. . 8 Jarrell Ken F. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 42 "13C chemical shifts" 44 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-12-14 update BMRB 'update residue names' 2020-08-06 original author 'original release' stop_ _Original_release_date 2020-01-30 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Identification of a novel N-linked glycan on the Archaellins and S-layer protein of the thermophilic methanogen, Methanothermococcus thermolithotrophicus ; _Citation_status 'in preparation' _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 Kelly John F. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . loop_ _Keyword 'glycan, post-translational modification, archaellin, S-layer protein, archaea, NMR, mass spectrometry' stop_ save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name 'heptameric archaellin N-glycan' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'heptameric archaellin N-glycan' $entity_1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class carbohydrate _Name_common entity_1 _Molecular_mass . _Mol_thiol_state 'not present' _Details 'This entry is missing ligand and/or non-standard residue chemical compound information.' ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ; XXXXXXX ; loop_ _Residue_seq_code _Residue_label 1 XA 2 XB 3 XC 4 XD 5 XE 6 XF 7 XG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source_1 _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 'Methanothermococcus thermolithotrophicus' 2186 Archaea . Methanothermococcus thermolithotrophicus stop_ save_ ######################### # Experimental source # ######################### save_experimental_source_1 _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name _Details $entity_1 'purified from the natural source' . . . . . ; The S-layer protein was isolated from the organism, digested with proteinase K and the glycopeptides were isolated by anion exchange chromatography for NMR analysis ; stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 3.2 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details ; With 5 mm Z-gradient probes with acetone internal reference (2.225 ppm for 1H and 31.45 ppm for 13C) using standard pulse sequences cosygpprqf (gCOSY), mlevphpr (TOCSY, mixing time 120 ms), roesyphpr (ROESY, mixing time 500 ms), hsqcedetgp (gHSQC), hsqcetgpml (gHSQC-TOCSY, 80 ms TOCSY delay) and hmbcgplpndqf (HMBC, 70 or 100 ms long range transfer delay). Spectral widths were 10 ppm for proton and 200 ppm for carbon observations respectively. Edited 1H-13C HSQC were recorded with 1500 data points in F2 and 256 in F1 with heteronuclear 1JC,H constant of 142.8 Hz (CH, CH3 signals were positive and CH2 signals were negative). Resolution was kept at < 3 Hz/pt in F2 in proton-proton correlations and 5 Hz/pt in F2 of H-C correlations. The spectra were processed and analysed using the Bruker Topspin version 2.1 program. ; save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 300 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _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 na C 13 'methyl carbon' ppm 31.45 internal direct . . . 1 na H 1 protons ppm 2.225 internal direct . . . 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-13C HSQC' '2D 1H-1H COSY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'heptameric archaellin N-glycan' _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 1 1 XA H1 H 4.790 0.005 1 2 1 1 XA H2 H 3.610 0.005 1 3 1 1 XA H3 H 3.790 0.005 1 4 1 1 XA H4 H 5.670 0.005 1 5 1 1 XA H7 H 1.570 0.005 1 6 1 1 XA C1 C 102.2 0.050 1 7 1 1 XA C2 C 71.90 0.050 1 8 1 1 XA C3 C 79.10 0.050 1 9 1 1 XA C4 C 72.40 0.050 1 10 1 1 XA C5 C 81.80 0.050 1 11 1 1 XA C6 C 176.9 0.050 1 12 1 1 XA C7 C 19.10 0.050 1 13 2 2 XB H1 H 5.560 0.005 1 14 2 2 XB H2 H 4.160 0.005 1 15 2 2 XB H3 H 3.800 0.005 1 16 2 2 XB H4 H 3.530 0.005 1 17 2 2 XB H5 H 3.940 0.005 1 18 2 2 XB H6 H 3.790 0.005 1 19 2 2 XB H71 H 3.710 0.005 2 20 2 2 XB H72 H 3.850 0.005 2 21 2 2 XB C1 C 99.70 0.050 1 22 2 2 XB C2 C 66.80 0.050 1 23 2 2 XB C3 C 81.60 0.050 1 24 2 2 XB C4 C 67.40 0.050 1 25 2 2 XB C5 C 70.60 0.050 1 26 2 2 XB C6 C 81.50 0.050 1 27 2 2 XB C7 C 60.90 0.050 1 28 3 3 XC H1 H 5.490 0.005 1 29 3 3 XC H2 H 4.210 0.005 1 30 3 3 XC H3 H 4.020 0.005 1 31 3 3 XC H4 H 4.630 0.005 1 32 3 3 XC H5 H 4.890 0.005 1 33 3 3 XC C1 C 99.10 0.050 1 34 3 3 XC C2 C 49.80 0.050 1 35 3 3 XC C3 C 76.00 0.050 1 36 3 3 XC C4 C 66.40 0.050 1 37 3 3 XC C5 C 74.70 0.050 1 38 3 3 XC C6 C 176.2 0.050 1 39 4 4 XD H1 H 5.460 0.005 1 40 4 4 XD H2 H 4.120 0.005 1 41 4 4 XD H3 H 3.960 0.005 1 42 4 4 XD H4 H 4.570 0.005 1 43 4 4 XD H5 H 4.760 0.005 1 44 4 4 XD C1 C 96.80 0.050 1 45 4 4 XD C2 C 68.70 0.050 1 46 4 4 XD C3 C 71.40 0.050 1 47 4 4 XD C4 C 82.10 0.050 1 48 4 4 XD C5 C 73.00 0.050 1 49 4 4 XD C6 C 174.8 0.050 1 50 5 5 XE H1 H 5.330 0.005 1 51 5 5 XE H2 H 3.990 0.005 1 52 5 5 XE H3 H 4.030 0.005 1 53 5 5 XE H4 H 4.470 0.005 1 54 5 5 XE H5 H 4.230 0.005 1 55 5 5 XE C1 C 95.10 0.050 1 56 5 5 XE C2 C 72.10 0.050 1 57 5 5 XE C3 C 68.20 0.050 1 58 5 5 XE C4 C 79.90 0.050 1 59 5 5 XE C5 C 72.00 0.050 1 60 5 5 XE C6 C 174.0 0.050 1 61 6 6 XF H1 H 4.990 0.005 1 62 6 6 XF H2 H 4.310 0.005 1 63 6 6 XF H3 H 3.730 0.005 1 64 6 6 XF H4 H 3.910 0.005 1 65 6 6 XF H5 H 3.340 0.005 1 66 6 6 XF H61 H 3.770 0.005 2 67 6 6 XF H62 H 3.920 0.005 2 68 6 6 XF C1 C 102.6 0.050 1 69 6 6 XF C2 C 77.00 0.050 1 70 6 6 XF C3 C 74.20 0.050 1 71 6 6 XF C4 C 70.10 0.050 1 72 6 6 XF C5 C 78.30 0.050 1 73 6 6 XF C6 C 61.80 0.050 1 74 7 7 XG H1 H 5.120 0.005 1 75 7 7 XG H2 H 4.080 0.005 1 76 7 7 XG H3 H 3.930 0.005 1 77 7 7 XG H4 H 4.300 0.005 1 78 7 7 XG H5 H 3.780 0.005 1 79 7 7 XG H61 H 3.780 0.005 2 80 7 7 XG H62 H 3.780 0.005 2 81 7 7 XG C1 C 79.40 0.050 1 82 7 7 XG C2 C 50.70 0.050 1 83 7 7 XG C3 C 78.90 0.050 1 84 7 7 XG C4 C 65.50 0.050 1 85 7 7 XG C5 C 77.60 0.050 1 86 7 7 XG C6 C 62.3 0.050 1 stop_ save_