data_16458 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids ; _BMRB_accession_number 16458 _BMRB_flat_file_name bmr16458.str _Entry_type original _Submission_date 2009-08-19 _Accession_date 2009-08-19 _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 Tomaselli Simona . . 2 Ragona Laura . . 3 Zetta Lucia . . 4 Assfalg Michael . . 5 Ferranti Pasquale . . 6 Longhi Renato . . 7 Bonvin Alexandre M.J.J. . 8 Molinari Henriette . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count binding_constants 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-03-08 original author . stop_ _Original_release_date 2010-03-08 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17607743 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tomaselli Simona . . 2 Ragona Laura . . 3 Zetta Lucia . . 4 Assfalg Michael . . 5 Ferranti Pasquale . . 6 Longhi Renato . . 7 Bonvin Alexandre M.J.J. . 8 Molinari Henriette . . stop_ _Journal_abbreviation Proteins _Journal_volume 69 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 177 _Page_last 191 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'cL-BABP GCDA complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label cL-BABP $cL-BABP GCDA $CHO 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_cL-BABP _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cL-BABP _Molecular_mass . _Mol_thiol_state 'not reported' _Details 'chicken liver bile acid binding protein' ############################## # Polymer residue sequence # ############################## _Residue_count 125 _Mol_residue_sequence ; AFSGTWQVYAQENYEEFLKA LALPEDLIKMARDIKPIVEI QQKGDDFVVTSKTPRQTVTN SFTLGKEADITTMDGKKLKC TVHLANGKLVTKSEKFSHEQ EVKGNEMVETITFGGVTLIR RSKRV ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 PHE 3 SER 4 GLY 5 THR 6 TRP 7 GLN 8 VAL 9 TYR 10 ALA 11 GLN 12 GLU 13 ASN 14 TYR 15 GLU 16 GLU 17 PHE 18 LEU 19 LYS 20 ALA 21 LEU 22 ALA 23 LEU 24 PRO 25 GLU 26 ASP 27 LEU 28 ILE 29 LYS 30 MET 31 ALA 32 ARG 33 ASP 34 ILE 35 LYS 36 PRO 37 ILE 38 VAL 39 GLU 40 ILE 41 GLN 42 GLN 43 LYS 44 GLY 45 ASP 46 ASP 47 PHE 48 VAL 49 VAL 50 THR 51 SER 52 LYS 53 THR 54 PRO 55 ARG 56 GLN 57 THR 58 VAL 59 THR 60 ASN 61 SER 62 PHE 63 THR 64 LEU 65 GLY 66 LYS 67 GLU 68 ALA 69 ASP 70 ILE 71 THR 72 THR 73 MET 74 ASP 75 GLY 76 LYS 77 LYS 78 LEU 79 LYS 80 CYS 81 THR 82 VAL 83 HIS 84 LEU 85 ALA 86 ASN 87 GLY 88 LYS 89 LEU 90 VAL 91 THR 92 LYS 93 SER 94 GLU 95 LYS 96 PHE 97 SER 98 HIS 99 GLU 100 GLN 101 GLU 102 VAL 103 LYS 104 GLY 105 ASN 106 GLU 107 MET 108 VAL 109 GLU 110 THR 111 ILE 112 THR 113 PHE 114 GLY 115 GLY 116 VAL 117 THR 118 LEU 119 ILE 120 ARG 121 ARG 122 SER 123 LYS 124 ARG 125 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-02-05 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 15084 cl-BABP 100.00 125 100.00 100.00 1.33e-85 BMRB 15854 Gd(III)-chelate 100.00 125 100.00 100.00 1.33e-85 BMRB 16309 holo_T91C 100.00 125 99.20 99.20 8.08e-85 BMRB 16310 cL-BABP_T91C 100.00 125 99.20 99.20 8.08e-85 BMRB 17767 cl_BABP 100.00 125 99.20 99.20 8.08e-85 PDB 1MVG "Nmr Solution Structure Of Chicken Liver Basic Fatty Acid Binding Protein (Lb-Fabp)" 100.00 125 100.00 100.00 1.33e-85 PDB 1TVQ "Crystal Structure Of Apo Chicken Liver Basic Fatty Acid Binding Protein (Or Bile Acid Binding Protein)" 100.00 125 100.00 100.00 1.33e-85 PDB 1TW4 "Crystal Structure Of Chicken Liver Basic Fatty Acid Binding Protein (Bile Acid Binding Protein) Complexed With Cholic Acid" 100.00 125 100.00 100.00 1.33e-85 PDB 1ZRY "Nmr Structural Analysis Of Apo Chicken Liver Bile Acid Binding Protein" 100.00 125 100.00 100.00 1.33e-85 PDB 2JN3 "Nmr Structure Of Cl-Babp Complexed To Chenodeoxycholic Acid" 100.00 125 100.00 100.00 1.33e-85 PDB 2K62 "Nmr Solution Structure Of The Supramolecular Adduct Between A Liver Cytosolic Bile Acid Binding Protein And A Bile Acid-Based G" 100.00 125 100.00 100.00 1.33e-85 PDB 2LFO "Nmr Structure Of Cl-BabpSS COMPLEXED WITH GLYCOCHENODEOXYCHOLIC AND Glycocholic Acids" 100.00 125 99.20 99.20 8.08e-85 GB AAK58094 "liver basic fatty acid binding protein [Gallus gallus]" 100.00 126 99.20 99.20 7.09e-85 GB ADE59142 "liver basic fatty acid binding protein [synthetic construct]" 100.00 135 99.20 99.20 8.34e-85 GB ADE59143 "liver basic fatty acid binding protein [synthetic construct]" 100.00 135 100.00 100.00 1.26e-85 GB ADE59144 "liver basic fatty acid binding protein [synthetic construct]" 100.00 135 100.00 100.00 1.26e-85 GB ADE59145 "liver basic fatty acid binding protein [synthetic construct]" 100.00 135 100.00 100.00 1.26e-85 PRF 2106165A "fatty acid-binding protein [Gallus gallus]" 100.00 125 100.00 100.00 1.33e-85 REF NP_989965 "fatty acid-binding protein, liver [Gallus gallus]" 100.00 126 99.20 99.20 7.09e-85 SP P80226 "RecName: Full=Fatty acid-binding protein, liver; AltName: Full=Fatty acid-binding protein 1; AltName: Full=Liver basic FABP; Sh" 100.00 126 100.00 100.00 9.71e-86 stop_ save_ save_CHO _Saveframe_category monomeric_polymer _Mol_type polymer _Name_common CHO _Molecular_mass . _Mol_thiol_state . _Details . _Residue_count . _Mol_residue_sequence . loop_ _Residue_seq_code _Residue_label 1 CHO stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_CHO _Saveframe_category polymer_residue _Mol_type D-SACCHARIDE _Name_common 'GLYCOCHENODEOXYCHOLIC ACID' _BMRB_code . _PDB_code CHO _Standard_residue_derivative . _Molecular_mass 449.623 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Nov 10 14:55:57 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? O3 O3 O . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? O7 O7 O . 0 . ? C8 C8 C . 0 . ? C9 C9 C . 0 . ? C10 C10 C . 0 . ? C11 C11 C . 0 . ? C12 C12 C . 0 . ? C13 C13 C . 0 . ? C14 C14 C . 0 . ? C15 C15 C . 0 . ? C16 C16 C . 0 . ? C17 C17 C . 0 . ? C18 C18 C . 0 . ? C19 C19 C . 0 . ? C20 C20 C . 0 . ? C21 C21 C . 0 . ? C22 C22 C . 0 . ? C23 C23 C . 0 . ? C24 C24 C . 0 . ? O24 O24 O . 0 . ? N25 N25 N . 0 . ? C26 C26 C . 0 . ? C27 C27 C . 0 . ? OT1 OT1 O . 0 . ? OT2 OT2 O . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H3 H3 H . 0 . ? HO3 HO3 H . 0 . ? H41 H41 H . 0 . ? H42 H42 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H7 H7 H . 0 . ? HO7 HO7 H . 0 . ? H8 H8 H . 0 . ? H9 H9 H . 0 . ? H111 H111 H . 0 . ? H112 H112 H . 0 . ? H121 H121 H . 0 . ? H122 H122 H . 0 . ? H14 H14 H . 0 . ? H151 H151 H . 0 . ? H152 H152 H . 0 . ? H161 H161 H . 0 . ? H162 H162 H . 0 . ? H17 H17 H . 0 . ? H181 H181 H . 0 . ? H182 H182 H . 0 . ? H183 H183 H . 0 . ? H191 H191 H . 0 . ? H192 H192 H . 0 . ? H193 H193 H . 0 . ? H20 H20 H . 0 . ? H211 H211 H . 0 . ? H212 H212 H . 0 . ? H213 H213 H . 0 . ? H221 H221 H . 0 . ? H222 H222 H . 0 . ? H231 H231 H . 0 . ? H232 H232 H . 0 . ? HN HN H . 0 . ? H261 H261 H . 0 . ? H262 H262 H . 0 . ? HOT HOT 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 SING C1 C2 ? ? SING C1 C10 ? ? SING C1 H11 ? ? SING C1 H12 ? ? SING C2 C3 ? ? SING C2 H21 ? ? SING C2 H22 ? ? SING C3 O3 ? ? SING C3 C4 ? ? SING C3 H3 ? ? SING O3 HO3 ? ? SING C4 C5 ? ? SING C4 H41 ? ? SING C4 H42 ? ? SING C5 C6 ? ? SING C5 C10 ? ? SING C5 H5 ? ? SING C6 C7 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING C7 O7 ? ? SING C7 C8 ? ? SING C7 H7 ? ? SING O7 HO7 ? ? SING C8 C9 ? ? SING C8 C14 ? ? SING C8 H8 ? ? SING C9 C10 ? ? SING C9 C11 ? ? SING C9 H9 ? ? SING C10 C19 ? ? SING C11 C12 ? ? SING C11 H111 ? ? SING C11 H112 ? ? SING C12 C13 ? ? SING C12 H121 ? ? SING C12 H122 ? ? SING C13 C14 ? ? SING C13 C17 ? ? SING C13 C18 ? ? SING C14 C15 ? ? SING C14 H14 ? ? SING C15 C16 ? ? SING C15 H151 ? ? SING C15 H152 ? ? SING C16 C17 ? ? SING C16 H161 ? ? SING C16 H162 ? ? SING C17 C20 ? ? SING C17 H17 ? ? SING C18 H181 ? ? SING C18 H182 ? ? SING C18 H183 ? ? SING C19 H191 ? ? SING C19 H192 ? ? SING C19 H193 ? ? SING C20 C21 ? ? SING C20 C22 ? ? SING C20 H20 ? ? SING C21 H211 ? ? SING C21 H212 ? ? SING C21 H213 ? ? SING C22 C23 ? ? SING C22 H221 ? ? SING C22 H222 ? ? SING C23 C24 ? ? SING C23 H231 ? ? SING C23 H232 ? ? DOUB C24 O24 ? ? SING C24 N25 ? ? SING N25 C26 ? ? SING N25 HN ? ? SING C26 C27 ? ? SING C26 H261 ? ? SING C26 H262 ? ? DOUB C27 OT1 ? ? SING C27 OT2 ? ? SING OT2 HOT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $cL-BABP 'E. coli' 562 Eubacteria . Escherichia coli 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 $cL-BABP 'purified from the natural source' . Escherichia coli . . 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $cL-BABP 0.5 mM . . 'natural abundance' $CHO . mM 0.15 3.75 'natural abundance' 'phosphate buffer' 30 mM . . 'natural abundance' D2O 5 % . . 'natural abundance' H2O 95 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version 5.0.3 loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'peak volume integration' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'docking calculation' stop_ _Details . save_ save_TALOS _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_HADDOCK _Saveframe_category software _Name HADDOCK _Version 2.0_devel loop_ _Vendor _Address _Electronic_address '(Dominguez C, oelens R, Bonvin AM., 2003)' . . stop_ loop_ _Task 'docking calculation' stop_ _Details . save_ save_LIGPLOT _Saveframe_category software _Name LIGPLOT _Version . loop_ _Vendor _Address _Electronic_address '(Wallace AC, Laskowski RA, Thornton JM., 1995)' . . stop_ loop_ _Task visualization/analysis stop_ _Details . save_ save_PROFIT _Saveframe_category software _Name PROFIT _Version . loop_ _Vendor _Address _Electronic_address '(Martin, A. C. R., Profit)' . . stop_ loop_ _Task 'global superposition of backbone atoms' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_HMBC_1 _Saveframe_category NMR_applied_experiment _Experiment_name HMBC _Sample_label $sample_1 save_ save_3D_1H-15N_HSQC-NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N HSQC-NOESY' _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 7.2 . pH pressure 1 . atm temperature 298 . K stop_ save_