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- PDB-2jn3: NMR structure of cl-BABP complexed to chenodeoxycholic acid -

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Basic information

Entry
Database: PDB / ID: 2jn3
TitleNMR structure of cl-BABP complexed to chenodeoxycholic acid
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / BILE ACIDS
Function / homology
Function and homology information


fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CHENODEOXYCHOLIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
AuthorsEliseo, T. / Ragona, L. / Catalano, M. / Assfalf, M. / Paci, M. / Zetta, L. / Molinari, H. / Cicero, D.O.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and dynamic determinants of ligand binding in the ternary complex of chicken liver bile acid binding protein with two bile salts revealed by NMR
Authors: Eliseo, T. / Ragona, L. / Catalano, M. / Assfalg, M. / Paci, M. / Zetta, L. / Molinari, H. / Cicero, D.O.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8853
Polymers14,1001
Non-polymers7852
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Fatty acid-binding protein, liver / L-FABP / Liver basic FABP / LB- FABP / Liver bile acid-binding protein / L-BABP


Mass: 14100.177 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: FABP1 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P80226
#2: Chemical ChemComp-JN3 / CHENODEOXYCHOLIC ACID / (3ALPHA,5ALPHA,7BETA,8ALPHA,17ALPHA)-3,7-DIHYDROXYCHOLAN-24-OIC ACID


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
2623D (H)CCH-TOCSY
2723D (H)CCH-TOCSY
1813D 1H-13C NOESY
1913D 1H-15N TOCSY
11013D 1H-15N NOESY
11113D HBHA(CO)NH
21223D 13C-edited 13C-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] cl-BABP, 3 mM CDA, 90% H2O, 10% D2O90% H2O/10% D2O
21.2 mM [U-100% 13C; U-100% 15N] cl-BABP, 3 mM CDA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMcl-BABP[U-100% 13C; U-100% 15N]1
3 mMCDA1
1.2 mMcl-BABP[U-100% 13C; U-100% 15N]2
3 mMCDA2
1.2 mMcl-BABP[U-100% 13C; U-100% 15N]3
3 mMCDA3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.15 7.0 ambient 298 K
20.45 7.0 ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE4002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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