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- PDB-1zry: NMR structural analysis of apo chicken liver bile acid binding protein -

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Basic information

Entry
Database: PDB / ID: 1zry
TitleNMR structural analysis of apo chicken liver bile acid binding protein
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / BETA BARREL
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
Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics, minimization
AuthorsRagona, L. / Catalano, M. / Luppi, M. / Cicero, D. / Eliseo, T. / Foote, J. / Fogolari, F. / Zetta, L. / Molinari, H.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: NMR Dynamic Studies Suggest that Allosteric Activation Regulates Ligand Binding in Chicken Liver Bile Acid-binding Protein
Authors: Ragona, L. / Catalano, M. / Luppi, M. / Cicero, D. / Eliseo, T. / Foote, J. / Fogolari, F. / Zetta, L. / Molinari, H.
History
DepositionMay 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,1001
Polymers14,1001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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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) / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P80226

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY, NOESY
1212D 1H-15N HSQC, 3D 1H-15N HSQC-TOCSY,1H-15N HSQC-NOESY, 3D HNHA
1313D 1H-15N-13C HNCA, HN(CO)CA,HNCO,CBCANH, CBCA(CO)NH
1423D 1H-15N-13C NOESY optimised for aromatic and aliphatic residues
1523D HACACO, (H)CCH-COSY, (H)CCH-TOCSY, H(C)CH-COSY, H(C)CHTOCSY
2612D TOCSY, NOESY,2D 1H-15N HSQC, 3D 1H-15N HSQC-TOCSY,1H-15N HSQC-NOESY, 3D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM chicken liver bile acid binding protein 15N, 13C, 20 mM phosphate buffer Na90% H2O/10% D2O
21 mM chicken liver bile acid binding protein 15N, 13C, 20 mM phosphate buffer NaD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM 7.0 ambient 298 K
220 mM 5.6 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 DRXBrukerDRX5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE7003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker softwarecollection
NMRPipe2.2Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) J Biomol NMR 6, 277-29data analysis
NMRView5Johnson, B.A. and Blevins, R.A. J. Biomolecular NMR 4, 603 1994data analysis
DYANA1.4Guntert, P., Mumenthaler, C., and Wuthrich, K. (1997) J Mol Biol 273, 283-298structure solution
Discover97Molecular Simulations, San diego, CArefinement
RefinementMethod: torsion angle dynamics, minimization / Software ordinal: 1
Details: the structures are based on a set of 1000 non redundant NOEs ; 26 distance restraints for 13 backbone hydrogen bonds; 48 phi angle constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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