data_17718 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Hydrogen Exchange in Unligated and Ligated Straphlococcal Nuclease ; _BMRB_accession_number 17718 _BMRB_flat_file_name bmr17718.str _Entry_type original _Submission_date 2011-06-17 _Accession_date 2011-06-17 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; Measured the exchange kinetics over 70% of 143 backbone amide hydrogens in staphylococcal nuclease H124L. The measurement of hydrogen exchange kinetics provided a basis for interpreting the changes in stability and dynamics afforded by inhibitor binding. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Markley John L. . 2 Loh Stewart N. . 3 Prehoda Kenneth E. . 4 Wang Jinfeng . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count H_exch_rates 2 stop_ loop_ _Data_type _Data_type_count "H exchange rates" 115 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-01-24 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 5003 'Entry containing chemical shifts of staphylococcal nuclease H124L.' stop_ _Original_release_date 2011-06-24 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Hydrogen exchange in unligated and ligated staphylococcal nuclease ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8218167 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Markley John L. . 2 Loh Stewart N. . 3 Prehoda Kenneth E. . 4 Wang Jinfeng . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 32 _Journal_issue 41 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11022 _Page_last 11028 _Year 1993 _Details . loop_ _Keyword NMR stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name staph-nucl-H124L _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Staphylococcal_nuclease $Staphylococcal_nuclease 'Calcium ion' $CA pdTp $entity_THP 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_Staphylococcal_nuclease _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Staphylococcal_nuclease _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'Useful for studying protein folding' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 149 _Mol_residue_sequence ; ATSTKKLHKEPATLIKAIDG DTVKLMYKGQPMTFRLLLVD TPETKHPKKGVEKYGPEASA FTKKMVENAKKIEVEFDKGQ RTDKYGRGLAYIYADGKMVN EALVRQGLAKVAYVYKPNNT HEQLLRKSEAQAKKEKLNIW SEDNADSGQ ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ALA 2 2 THR 3 3 SER 4 4 THR 5 5 LYS 6 6 LYS 7 7 LEU 8 8 HIS 9 9 LYS 10 10 GLU 11 11 PRO 12 12 ALA 13 13 THR 14 14 LEU 15 15 ILE 16 16 LYS 17 17 ALA 18 18 ILE 19 19 ASP 20 20 GLY 21 21 ASP 22 22 THR 23 23 VAL 24 24 LYS 25 25 LEU 26 26 MET 27 27 TYR 28 28 LYS 29 29 GLY 30 30 GLN 31 31 PRO 32 32 MET 33 33 THR 34 34 PHE 35 35 ARG 36 36 LEU 37 37 LEU 38 38 LEU 39 39 VAL 40 40 ASP 41 41 THR 42 42 PRO 43 43 GLU 44 44 THR 45 45 LYS 46 46 HIS 47 47 PRO 48 48 LYS 49 49 LYS 50 50 GLY 51 51 VAL 52 52 GLU 53 53 LYS 54 54 TYR 55 55 GLY 56 56 PRO 57 57 GLU 58 58 ALA 59 59 SER 60 60 ALA 61 61 PHE 62 62 THR 63 63 LYS 64 64 LYS 65 65 MET 66 66 VAL 67 67 GLU 68 68 ASN 69 69 ALA 70 70 LYS 71 71 LYS 72 72 ILE 73 73 GLU 74 74 VAL 75 75 GLU 76 76 PHE 77 77 ASP 78 78 LYS 79 79 GLY 80 80 GLN 81 81 ARG 82 82 THR 83 83 ASP 84 84 LYS 85 85 TYR 86 86 GLY 87 87 ARG 88 88 GLY 89 89 LEU 90 90 ALA 91 91 TYR 92 92 ILE 93 93 TYR 94 94 ALA 95 95 ASP 96 96 GLY 97 97 LYS 98 98 MET 99 99 VAL 100 100 ASN 101 101 GLU 102 102 ALA 103 103 LEU 104 104 VAL 105 105 ARG 106 106 GLN 107 107 GLY 108 108 LEU 109 109 ALA 110 110 LYS 111 111 VAL 112 112 ALA 113 113 TYR 114 114 VAL 115 115 TYR 116 116 LYS 117 117 PRO 118 118 ASN 119 119 ASN 120 120 THR 121 121 HIS 122 122 GLU 123 123 GLN 124 124 LEU 125 125 LEU 126 126 ARG 127 127 LYS 128 128 SER 129 129 GLU 130 130 ALA 131 131 GLN 132 132 ALA 133 133 LYS 134 134 LYS 135 135 GLU 136 136 LYS 137 137 LEU 138 138 ASN 139 139 ILE 140 140 TRP 141 141 SER 142 142 GLU 143 143 ASP 144 144 ASN 145 145 ALA 146 146 ASP 147 147 SER 148 148 GLY 149 149 GLN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_CA _Saveframe_category ligand _Mol_type non-polymer _Name_common "CA (CALCIUM ION)" _BMRB_code . _PDB_code CA _Molecular_mass 40.078 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Jun 15 15:31:50 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CA CA CA . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ save_THP _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common THYMIDINE-3',5'-DIPHOSPHATE _BMRB_code THP _PDB_code THP _Molecular_mass 402.188 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P2 P2 P . 0 . ? O4P O4P O . 0 . ? O5P O5P O . 0 . ? O6P O6P O . 0 . ? P1 P1 P . 0 . ? O1P O1P O . 0 . ? O2P O2P O . 0 . ? O3P O3P O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? C1' C1' C . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? C5 C5 C . 0 . ? C5M C5M C . 0 . ? C6 C6 C . 0 . ? HOP5 HOP5 H . 0 . ? HOP6 HOP6 H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? H2'1 H2'1 H . 0 . ? H2'2 H2'2 H . 0 . ? H1' H1' H . 0 . ? H3 H3 H . 0 . ? H51 H51 H . 0 . ? H52 H52 H . 0 . ? H53 H53 H . 0 . ? H6 H6 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB P2 O4P ? ? SING P2 O5P ? ? SING P2 O6P ? ? SING P2 O5' ? ? SING O5P HOP5 ? ? SING O6P HOP6 ? ? DOUB P1 O1P ? ? SING P1 O2P ? ? SING P1 O3P ? ? SING P1 O3' ? ? SING O2P HOP2 ? ? SING O3P HOP3 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING C2' C1' ? ? SING C2' H2'1 ? ? SING C2' H2'2 ? ? SING C1' N1 ? ? SING C1' H1' ? ? SING N1 C2 ? ? SING N1 C6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING N3 C4 ? ? SING N3 H3 ? ? DOUB C4 O4 ? ? SING C4 C5 ? ? SING C5 C5M ? ? DOUB C5 C6 ? ? SING C5M H51 ? ? SING C5M H52 ? ? SING C5M H53 ? ? SING C6 H6 ? ? 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 _Strain $Staphylococcal_nuclease 'Staphylococcus aureus' 1280 Bacteria . Staphylococcus aureus 'V8 strain' 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 $Staphylococcal_nuclease 'recombinant technology' . Escherichia coli . 'modified pTSN2cc' 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 $Staphylococcal_nuclease 3.0 mM 'natural abundance' $entity_THP 9.0 mM 'natural abundance' succinate-d4 50 mM 'natural abundance' $CA 18 mM 'natural abundance' H2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_Bruker _Saveframe_category software _Name xwinnmr _Version AM500 loop_ _Vendor _Address _Electronic_address Bruker . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AM _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_HSMQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HSMQC' _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 pH 5.5 . pH pressure 1 . atm temperature 310 . K stop_ save_ save_H_exch_rates_1 _Saveframe_category H_exchange_rates _Details . loop_ _Experiment_label $2D_HSMQC_1 stop_ loop_ _Sample_label $sample_1 $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _H_exchange_rate_units h _Mol_system_component_name Staphylococcal_nuclease _Text_data_format . _Text_data . loop_ _Residue_seq_code _Residue_label _Atom_name _H_exchange_rate_value _H_exchange_rate_min_value _H_exchange_rate_max_value _H_exchange_rate_value_error 12 ALA H 39.3 . . 9.2 13 THR H 8.28 . . 1.1 16 LYS H 131 . . 12 21 ASP H 13 . . 4 23 VAL H 273 . . 47 24 LYS H 377 . . 44 25 LEU H 386 . . 110 26 MET H 679 . . 230 27 TYR H 14.3 . . 2.6 32 MET H 125 . . 17 34 PHE H 410 . . 95 35 ARG H 353 . . 97 37 LEU H 279 . . 100 38 LEU H 8.12 . . 0.90 39 VAL H 690 . . 240 40 ASP H 40.6 . . 4.0 61 PHE H 35.7 . . 2.7 62 THR H 139 . . 13 63 LYS H 124 . . 19 64 LYS H 203 . . 18 65 MET H 90.5 . . 14 66 VAL H 406 . . 87 67 GLU H 109 . . 9.9 69 ALA H 1.29 . . 0.047 71 LYS H 1.37 . . 0.40 73 GLU H 337 . . 87 74 VAL H 263 . . 42 75 GLU H 265 . . 87 76 PHE H 2.23 . . 0.32 77 ASP H 16.2 . . 2.40 78 LYS H 1.82 . . 0.19 83 ASP H 41.8 . . 6.1 88 GLY H 76.9 . . 11 89 LEU H 554 . . 390 90 ALA H 535 . . 220 91 TYR H 763 . . 290 93 TYR H 1100 . . 900 94 ALA H 437 . . 91 97 LYS H 58.7 . . 2.6 99 VAL H 388 . . 71 100 ASN H 244 . . 24 101 GLU H 280 . . 44 102 ALA H 249 . . 84 103 LEU H 298 . . 69 104 VAL H 630 . . 170 105 ARG H 264 . . 44 106 GLN H 209 . . 22 107 GLY H 126 . . 15 108 LEU H 148 . . 18 109 ALA H 244 . . 53 111 VAL H 2.98 . . 0.22 122 GLU H 0.95 . . 0.2 125 LEU H 122 . . 12 126 ARG H 96.7 . . 6.7 127 LYS H 2.61 . . 0.20 128 SER H 2.43 . . 0.27 129 GLU H 115 . . 9.9 130 ALA H 95.3 . . 7.5 131 GLN H 3.99 . . 0.23 132 ALA H 177 . . 34 133 LYS H 151 . . 11 134 LYS H 91.9 . . 6.6 135 GLU H 21.0 . . 7.3 136 LYS H 35.2 . . 4.3 138 ASN H 74.6 . . 25 141 SER H 8.33 . . 1.5 stop_ save_ save_H_exch_rates_2 _Saveframe_category H_exchange_rates _Details . loop_ _Experiment_label $2D_HSMQC_1 stop_ loop_ _Sample_label $sample_1 $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _H_exchange_rate_units h _Mol_system_component_name Staphylococcal_nuclease _Text_data_format . _Text_data . loop_ _Residue_seq_code _Residue_label _Atom_name _H_exchange_rate_value _H_exchange_rate_min_value _H_exchange_rate_max_value _H_exchange_rate_value_error 12 ALA H 3.38 . . 0.32 13 THR H 1.72 . . 0.12 15 ILE H 15.6 . . 1.8 16 LYS H 5.3 . . 0.7 22 THR H 9.71 . . 0.88 23 VAL H 19.1 . . 1.3 24 LYS H 25.0 . . 1.9 25 LEU H 23.9 . . 2.3 26 MET H 22.0 . . 2.4 27 TYR H 4.25 . . 0.63 30 GLN H 4.50 . . 0.51 34 PHE H 16.0 . . 4.3 37 LEU H 42.0 . . 7.6 39 VAL H 19.4 . . 1.2 61 PHE H 2.93 . . 0.26 62 THR H 4.40 . . 0.32 64 LYS H 5.82 . . 0.27 65 MET H 5.89 . . 0.23 66 VAL H 17.0 . . 1.1 67 GLU H 9.39 . . 0.60 73 GLU H 15.7 . . 1.1 74 VAL H 27.9 . . 2.7 75 GLU H 13.3 . . 1.5 89 LEU H 6.75 . . 1.1 90 ALA H 14.0 . . 1.8 91 TYR H 14.8 . . 1.3 92 ILE H 15.9 . . 1.7 93 TYR H 35.6 . . 9.4 94 ALA H 14.1 . . 1.3 99 VAL H 19.9 . . 2.0 100 ASN H 6.45 . . 0.40 101 GLU H 6.88 . . 0.22 104 VAL H 48 . . 5.2 105 ARG H 3.91 . . 1.3 106 GLN H 4.99 . . 0.66 107 GLY H 2.06 . . 0.44 108 LEU H 4.47 . . 0.62 109 ALA H 5.41 . . 0.51 111 VAL H 4.43 . . 0.28 125 LEU H 3.75 . . 0.31 126 ARG H 2.59 . . 0.044 129 GLU H 1.31 . . 0.18 130 ALA H 2.53 . . 0.11 131 GLN H 1.23 . . 0.11 132 ALA H 2.48 . . 0.27 133 LYS H 2.5 . . 0.13 135 GLU H 2.92 . . 0.55 136 LYS H 2.14 . . 0.29 137 LEU H 3.3 . . 0.28 stop_ save_