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- PDB-2lba: Solution structure of chicken ileal BABP in complex with glycoche... -

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Basic information

Entry
Database: PDB / ID: 2lba
TitleSolution structure of chicken ileal BABP in complex with glycochenodeoxycholic acid
ComponentsBABP protein
KeywordsLIPID BINDING PROTEIN / Ileal Bile Acid Binding Protein
Function / homology
Function and homology information


Recycling of bile acids and salts / Triglyceride catabolism / fatty acid transport / fatty acid binding / membrane / 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 / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsZanzoni, S. / Assfalg, M. / Giorgetti, A. / D'Onofrio, M. / Molinari, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Requirements for Cooperativity in Ileal Bile Acid-binding Proteins.
Authors: Zanzoni, S. / Assfalg, M. / Giorgetti, A. / D'Onofrio, M. / Molinari, H.
History
DepositionMar 28, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _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 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BABP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0743
Polymers15,1751
Non-polymers8992
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 #1lowest energy

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Components

#1: Protein BABP protein


Mass: 15175.220 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / Strain (production host): SG / References: UniProt: F1NUJ7*PLUS
#2: Chemical ChemComp-CHO / GLYCOCHENODEOXYCHOLIC ACID


Mass: 449.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C26H43NO5 / Comment: detergent*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1312D 1H-1H NOESY
1433D (H)CCH-TOCSY
1533D (H)CCH-TOCSY
1623D 1H-15N NOESY
1723D 1H-13C NOESY aliphatic
1833D 13C-edited 13C-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM Protein, 1.6 mM GLYCOCHENODEOXYCHOLIC ACID, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] Protein, 3.2 mM GLYCOCHENODEOXYCHOLIC ACID, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 13C; U-100% 15N] Protein, 3.2 mM GLYCOCHENODEOXYCHOLIC ACID, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMProtein-11
1.6 mMGLYCOCHENODEOXYCHOLIC ACID-21
0.8 mMProtein-3[U-100% 13C; U-100% 15N]2
3.2 mMGLYCOCHENODEOXYCHOLIC ACID-42
0.8 mMProtein-5[U-100% 13C; U-100% 15N]3
3.2 mMGLYCOCHENODEOXYCHOLIC ACID-63
Sample conditionsIonic strength: 30 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRView8.0.a.30Johnson, One Moon Scientificchemical shift assignment
TopSpin2.1Bruker Biospincollection
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
HADDOCK2.1Bonvinstructure solution
HADDOCK2.1Bonvinrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: refinement in explicit water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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