data_2067 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Characterization of Phosphate Binding in the Active Site of Barnase by Site-Directed Mutagenesis and NMR ; _BMRB_accession_number 2067 _BMRB_flat_file_name bmr2067.str _Entry_type update _Submission_date 1995-07-31 _Accession_date 1996-03-25 _Entry_origination BMRB _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 Meiering Elizabeth M. . 2 Bycroft Mark . . 3 Fersht Alan R. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 72 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-16 revision BMRB 'Complete natural source information' 1999-06-14 revision BMRB 'Converted to BMRB NMR-STAR V 2.1 format' 1996-03-25 reformat BMRB 'Converted to the BMRB 1996-03-01 STAR flat-file format' 1995-07-31 original BMRB 'Last release in original BMRB flat-file format' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Meiering, Elizabeth M., Bycroft, Mark, Fersht, Alan R., "Characterization of Phosphate Binding in the Active Site of Barnase by Site-Directed Mutagenesis and NMR," Biochemistry 30 (47), 11348-11356 (1991). ; _Citation_title ; Characterization of Phosphate Binding in the Active Site of Barnase by Site-Directed Mutagenesis and NMR ; _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 Meiering Elizabeth M. . 2 Bycroft Mark . . 3 Fersht Alan R. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 30 _Journal_issue 47 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11348 _Page_last 11356 _Year 1991 _Details . save_ ################################## # Molecular system description # ################################## save_system_barnase _Saveframe_category molecular_system _Mol_system_name barnase _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label barnase $barnase stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic ? _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_barnase _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common barnase _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 110 _Mol_residue_sequence ; AQVINTFDGVADYLQTYHKL PDNYITKSEAQALGWVASKG NLADVAPGKSIGGDIFSNRE GKLPGKSGRTWREADINYTS GFRNSDRILYSSDWLIYKTT DHYQTFTKIR ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 GLN 3 VAL 4 ILE 5 ASN 6 THR 7 PHE 8 ASP 9 GLY 10 VAL 11 ALA 12 ASP 13 TYR 14 LEU 15 GLN 16 THR 17 TYR 18 HIS 19 LYS 20 LEU 21 PRO 22 ASP 23 ASN 24 TYR 25 ILE 26 THR 27 LYS 28 SER 29 GLU 30 ALA 31 GLN 32 ALA 33 LEU 34 GLY 35 TRP 36 VAL 37 ALA 38 SER 39 LYS 40 GLY 41 ASN 42 LEU 43 ALA 44 ASP 45 VAL 46 ALA 47 PRO 48 GLY 49 LYS 50 SER 51 ILE 52 GLY 53 GLY 54 ASP 55 ILE 56 PHE 57 SER 58 ASN 59 ARG 60 GLU 61 GLY 62 LYS 63 LEU 64 PRO 65 GLY 66 LYS 67 SER 68 GLY 69 ARG 70 THR 71 TRP 72 ARG 73 GLU 74 ALA 75 ASP 76 ILE 77 ASN 78 TYR 79 THR 80 SER 81 GLY 82 PHE 83 ARG 84 ASN 85 SER 86 ASP 87 ARG 88 ILE 89 LEU 90 TYR 91 SER 92 SER 93 ASP 94 TRP 95 LEU 96 ILE 97 TYR 98 LYS 99 THR 100 THR 101 ASP 102 HIS 103 TYR 104 GLN 105 THR 106 PHE 107 THR 108 LYS 109 ILE 110 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-25 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 16169 barnase 98.18 108 99.07 99.07 4.02e-71 BMRB 16170 barnase 98.18 108 99.07 99.07 4.02e-71 BMRB 16171 barnase 98.18 108 99.07 99.07 4.02e-71 BMRB 16172 barnase 98.18 108 99.07 99.07 4.02e-71 BMRB 2066 barnase 100.00 110 100.00 100.00 5.94e-74 BMRB 2070 barnase 100.00 110 100.00 100.00 5.94e-74 PDB 1A2P "Barnase Wildtype Structure At 1.5 Angstroms Resolution" 100.00 110 100.00 100.00 5.94e-74 PDB 1B20 "Deletion Of A Buried Salt-Bridge In Barnase" 100.00 110 99.09 99.09 4.19e-73 PDB 1B21 "Deletion Of A Buried Salt Bridge In Barnase" 100.00 110 98.18 99.09 1.52e-72 PDB 1B27 "Structural Response To Mutation At A Protein-Protein Interface" 100.00 110 100.00 100.00 5.94e-74 PDB 1B2S "Structural Response To Mutation At A Protein-Protein Interface" 100.00 110 99.09 99.09 2.89e-73 PDB 1B2U "Structural Response To Mutation At A Protein-Protein Interface" 100.00 110 99.09 99.09 2.89e-73 PDB 1B2X "Barnase Wildtype Structure At Ph 7.5 From A Cryo_cooled Crystal At 100k" 100.00 110 100.00 100.00 5.94e-74 PDB 1B2Z "Deletion Of A Buried Salt Bridge In Barnase" 100.00 110 99.09 100.00 2.08e-73 PDB 1B3S "Structural Response To Mutation At A Protein-Protein Interface" 100.00 110 99.09 99.09 9.10e-73 PDB 1BAN "The Contribution Of Buried Hydrogen Bonds To Protein Stability: The Crystal Structures Of Two Barnase Mutants" 100.00 110 99.09 100.00 1.25e-73 PDB 1BAO "The Contribution Of Buried Hydrogen Bonds To Protein Stability: The Crystal Structures Of Two Barnase Mutants" 100.00 110 99.09 100.00 1.35e-73 PDB 1BGS "Recognition Between A Bacterial Ribonuclease, Barnase, And Its Natural Inhibitor, Barstar" 100.00 110 100.00 100.00 5.94e-74 PDB 1BNE "Barnase A43cS80C DISULFIDE MUTANT" 100.00 110 98.18 98.18 4.15e-73 PDB 1BNF "Barnase T70cS92C DISULFIDE MUTANT" 100.00 110 98.18 98.18 4.67e-73 PDB 1BNG "Barnase S85cH102C DISULFIDE MUTANT" 100.00 110 98.18 98.18 2.86e-72 PDB 1BNI "Barnase Wildtype Structure At Ph 6.0" 100.00 110 100.00 100.00 5.94e-74 PDB 1BNJ "Barnase Wildtype Structure At Ph 9.0" 100.00 110 100.00 100.00 5.94e-74 PDB 1BNR Barnase 100.00 110 100.00 100.00 5.94e-74 PDB 1BNS "Structural Studies Of Barnase Mutants" 100.00 110 99.09 99.09 2.23e-73 PDB 1BRG "Crystallographic Analysis Of Phe->leu Substitution In The Hydrophobic Core Of Barnase" 98.18 108 99.07 99.07 1.07e-71 PDB 1BRH "Barnase Mutant With Leu 14 Replaced By Ala" 100.00 110 99.09 99.09 2.80e-73 PDB 1BRI "Barnase Mutant With Ile 76 Replaced By Ala" 100.00 110 99.09 99.09 2.59e-73 PDB 1BRJ "Barnase Mutant With Ile 88 Replaced By Ala" 100.00 110 99.09 99.09 2.59e-73 PDB 1BRK "Barnase Mutant With Ile 96 Replaced By Ala" 100.00 110 99.09 99.09 2.59e-73 PDB 1BRN "Subsite Binding In An Rnase: Structure Of A Barnase- Tetranucleotide Complex At 1.76 Angstroms Resolution" 100.00 110 100.00 100.00 5.94e-74 PDB 1BRS "Protein-Protein Recognition: Crystal Structural Analysis Of A Barnase-Barstar Complex At 2.0-A Resolution" 100.00 110 100.00 100.00 5.94e-74 PDB 1BSA "Crystal Structural Analysis Of Mutations In The Hydrophobic Cores Of Barnase" 100.00 110 99.09 100.00 7.39e-74 PDB 1BSB "Crystal Structural Analysis Of Mutations In The Hydrophobic Cores Of Barnase" 100.00 110 99.09 100.00 7.39e-74 PDB 1BSC "Crystal Structural Analysis Of Mutations In The Hydrophobic Cores Of Barnase" 100.00 110 99.09 100.00 7.39e-74 PDB 1BSD "Crystal Structural Analysis Of Mutations In The Hydrophobic Cores Of Barnase" 100.00 110 99.09 100.00 7.39e-74 PDB 1BSE "Crystal Structural Analysis Of Mutations In The Hydrophobic Cores Of Barnase" 100.00 110 99.09 100.00 1.54e-73 PDB 1FW7 "Nmr Structure Of 15n-Labeled Barnase" 99.09 110 100.00 100.00 2.77e-73 PDB 1RNB "Crystal Structure Of A Barnase-D(GpC) Complex At 1.9 Angstroms Resolution" 100.00 110 98.18 100.00 1.47e-72 PDB 1X1U "Water-Mediate Interaction At Aprotein-Protein Interface" 100.00 110 100.00 100.00 5.94e-74 PDB 1X1W "Water-Mediate Interaction At Aprotein-Protein Interface" 100.00 110 100.00 100.00 5.94e-74 PDB 1X1X "Water-Mediate Interaction At Aprotein-Protein Interface" 100.00 110 100.00 100.00 5.94e-74 PDB 1X1Y "Water-Mediate Interaction At Aprotein-Protein Interface" 100.00 110 99.09 99.09 4.28e-73 PDB 1YVS "Trimeric Domain Swapped Barnase" 100.00 110 100.00 100.00 5.94e-74 PDB 2C4B "Inhibitor Cystine Knot Protein Mcoeeti Fused To The Catalytically Inactive Barnase Mutant H102a" 99.09 143 99.08 99.08 1.74e-72 PDB 2F4Y "Barnase Cross-Linked With Glutaraldehyde" 98.18 108 100.00 100.00 1.81e-72 PDB 2F56 "Barnase Cross-Linked With Glutaraldehyde Soaked In 6m Urea" 98.18 108 100.00 100.00 1.81e-72 PDB 2F5M "Cross-Linked Barnase Soaked In Bromo-Ethanol" 98.18 108 100.00 100.00 1.81e-72 PDB 2F5W "Cross-Linked Barnase Soaked In 3 M Thiourea" 98.18 108 100.00 100.00 1.81e-72 PDB 2KF3 "Barnase, Low Pressure Reference Nmr Structure" 100.00 110 99.09 99.09 9.10e-73 PDB 2KF4 "Barnase High Pressure Structure" 100.00 110 99.09 99.09 9.10e-73 PDB 2KF5 "Barnase Bound To D(Cgac), Low Pressure" 100.00 110 99.09 99.09 9.10e-73 PDB 2KF6 "Barnase Bound To D(Cgac) High Pressure" 100.00 110 99.09 99.09 9.10e-73 PDB 2ZA4 "Crystal Structural Analysis Of Barnase-barstar Complex" 100.00 110 99.09 99.09 2.89e-73 PDB 3KCH "Baranase Crosslinked By Glutaraldehyde" 100.00 110 100.00 100.00 5.94e-74 EMBL CAA31365 "barnase [Bacillus amyloliquefaciens]" 100.00 110 100.00 100.00 5.94e-74 EMBL CBI44445 "putative ribonuclease RBAM_031940 [Bacillus amyloliquefaciens DSM 7]" 100.00 157 100.00 100.00 5.89e-75 EMBL CCF06756 "Ribonuclease Barnase [Bacillus methylotrophicus CAU B946]" 100.00 157 98.18 99.09 3.29e-73 EMBL CCG51396 "Ribonuclease Barnase [Bacillus methylotrophicus YAU B9601-Y2]" 100.00 157 97.27 99.09 4.61e-73 EMBL CDG27389 "Ribonuclease [Bacillus methylotrophicus UCMB5113]" 100.00 149 98.18 99.09 9.63e-74 GB AAA86441 "barnase (RNase) precursor [Bacillus amyloliquefaciens]" 100.00 149 100.00 100.00 5.97e-75 GB AAB28825 "RNase Bci=extracellular ribonuclease {EC 3.1.27.1} [Bacillus circulans, BCF 247, Peptide, 110 aa]" 100.00 110 97.27 98.18 1.16e-71 GB AAB29635 "RNase=extracellular ribonuclease [Bacillus circulans, Peptide, 110 aa]" 100.00 110 97.27 98.18 1.16e-71 GB AAC53661 "barnase [synthetic construct]" 100.00 111 100.00 100.00 3.75e-74 GB AAP41137 "barnase ribonuclease precursor [Cloning vector pHRBar-6]" 100.00 131 100.00 100.00 1.96e-74 PRF 1204204A barnase 100.00 157 100.00 100.00 4.68e-75 PRF 2004243A RNase 100.00 110 97.27 98.18 1.16e-71 PRF 721946A RNase 100.00 110 98.18 100.00 1.47e-72 REF WP_003151497 "MULTISPECIES: ribonuclease [Bacillus]" 100.00 157 98.18 99.09 3.29e-73 REF WP_007407419 "MULTISPECIES: ribonuclease [Bacillus]" 100.00 157 97.27 99.09 4.61e-73 REF WP_013353722 "MULTISPECIES: ribonuclease [Bacillus subtilis group]" 100.00 157 100.00 100.00 5.89e-75 REF WP_015387655 "MULTISPECIES: ribonuclease [Bacillus]" 100.00 157 98.18 99.09 1.06e-73 REF WP_016937826 "MULTISPECIES: ribonuclease [Bacillus]" 100.00 154 97.27 98.18 7.05e-72 SP P00648 "RecName: Full=Ribonuclease; AltName: Full=Barnase; AltName: Full=RNase Ba; Flags: Precursor" 100.00 157 100.00 100.00 4.68e-75 SP P35078 "RecName: Full=Ribonuclease; AltName: Full=RNase Bci" 100.00 110 97.27 98.18 1.16e-71 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $barnase . 1390 Bacteria . Bacillus amyloliquefaciens 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 $barnase 'not available' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_list _Saveframe_category NMR_spectrometer _Manufacturer unknown _Model unknown _Field_strength 0 _Details 'spectrometer information not available' save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label $sample_one save_ ####################### # Sample conditions # ####################### save_sample_condition_set_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.5 . na temperature 310 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_par_set_one _Saveframe_category chemical_shift_reference _Details 'The chemical shift reference is not available at this time.' 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_chemical_shift_assignment_data_set_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_condition_set_one _Chem_shift_reference_set_label $chem_shift_reference_par_set_one _Mol_system_component_name barnase _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 . 27 LYS H H 10.43 . 1 2 . 27 LYS HG2 H 1.53 . 1 3 . 27 LYS HG3 H 1.53 . 1 4 . 28 SER H H 9.21 . 1 5 . 30 ALA H H 8.83 . 1 6 . 40 GLY HA2 H 3.69 . 1 7 . 40 GLY HA3 H 3.69 . 1 8 . 41 ASN H H 7.54 . 1 9 . 42 LEU H H 8.16 . 1 10 . 50 SER H H 8.15 . 1 11 . 52 GLY HA2 H 4.07 . 1 12 . 52 GLY HA3 H 4.07 . 1 13 . 54 ASP H H 8.79 . 1 14 . 56 PHE H H 9.04 . 1 15 . 56 PHE HD1 H 6.8 . 1 16 . 56 PHE HD2 H 6.8 . 1 17 . 56 PHE HE1 H 6.47 . 1 18 . 56 PHE HE2 H 6.47 . 1 19 . 56 PHE HZ H 7.07 . 1 20 . 57 SER HA H 3.91 . 1 21 . 58 ASN H H 6.18 . 1 22 . 58 ASN HA H 3.94 . 1 23 . 62 LYS HA H 3.96 . 1 24 . 62 LYS HB2 H 1.83 . 2 25 . 62 LYS HB3 H 1.69 . 2 26 . 63 LEU H H 7.5 . 1 27 . 63 LEU HA H 3.86 . 1 28 . 63 LEU HG H -1.06 . 1 29 . 73 GLU H H 8.27 . 1 30 . 73 GLU HA H 6.23 . 1 31 . 74 ALA H H 9.1 . 1 32 . 76 ILE H H 7.67 . 1 33 . 83 ARG H H 8.12 . 1 34 . 83 ARG HB2 H 1.94 . 1 35 . 83 ARG HB3 H 1.94 . 1 36 . 83 ARG HE H 9.73 . 1 37 . 83 ARG HH11 H 6.53 . 1 38 . 83 ARG HH12 H 6.53 . 1 39 . 83 ARG HH21 H 6.53 . 1 40 . 83 ARG HH22 H 6.53 . 1 41 . 84 ASN H H 8.94 . 1 42 . 86 ASP H H 7.97 . 1 43 . 87 ARG H H 9.44 . 1 44 . 87 ARG HA H 5.67 . 1 45 . 87 ARG HB2 H 1.69 . 1 46 . 87 ARG HB3 H 1.69 . 1 47 . 87 ARG HE H 7.85 . 1 48 . 89 LEU HA H 5.93 . 1 49 . 89 LEU HD1 H .86 . 2 50 . 89 LEU HD2 H .53 . 2 51 . 90 TYR H H 9.26 . 1 52 . 96 ILE HA H 5.72 . 1 53 . 97 TYR H H 10.33 . 1 54 . 101 ASP HA H 4.88 . 1 55 . 102 HIS H H 8.77 . 1 56 . 102 HIS HA H 2.96 . 1 57 . 102 HIS HB2 H 2.61 . 1 58 . 102 HIS HB3 H 2.61 . 1 59 . 102 HIS HD2 H 8.77 . 1 60 . 102 HIS HE1 H 6.64 . 1 61 . 103 TYR H H 7.66 . 1 62 . 103 TYR HA H 3.25 . 1 63 . 103 TYR HB2 H 3.53 . 1 64 . 103 TYR HB3 H 3.53 . 1 65 . 103 TYR HD1 H 6.7 . 1 66 . 103 TYR HD2 H 6.7 . 1 67 . 103 TYR HE1 H 6.46 . 1 68 . 103 TYR HE2 H 6.46 . 1 69 . 104 GLN H H 7.45 . 1 70 . 105 THR H H 9.91 . 1 71 . 108 LYS H H 8.99 . 1 72 . 110 ARG H H 8.28 . 1 stop_ save_