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- PDB-2lfo: NMR structure of cl-BABP/SS complexed with glycochenodeoxycholic ... -

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Basic information

Entry
Database: PDB / ID: 2lfo
TitleNMR structure of cl-BABP/SS complexed with glycochenodeoxycholic and glycocholic acids
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / heterotypic complex / bile acid binding protein / liver / bile acids / disulphide bridge
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
GLYCOCHOLIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsTomaselli, S. / Cogliati, C. / Pagano, K. / Zetta, L. / Zanzoni, S. / Assfalg, M. / Molinari, H. / Ragona, L.
CitationJournal: Chemistry / Year: 2012
Title: A disulfide bridge allows for site-selective binding in liver bile acid binding protein thereby stabilising the orientation of key amino acid side chains.
Authors: Tomaselli, S. / Assfalg, M. / Pagano, K. / Cogliati, C. / Zanzoni, S. / Molinari, H. / Ragona, L.
History
DepositionJul 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 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

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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)15,0173
Polymers14,1021
Non-polymers9152
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 / 50best HADDOCK score
RepresentativeModel #1lowest energy

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Components

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


Mass: 14102.216 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: FABP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P80226
#2: Chemical ChemComp-GCH / GLYCOCHOLIC ACID / N-CHOLYLGLYCINE


Mass: 465.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H43NO6
#3: Chemical ChemComp-CHO / GLYCOCHENODEOXYCHOLIC ACID


Mass: 449.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H43NO5 / Comment: detergent*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The first 10 (1-10) structures of the deposited bundle correspond to cluster 2( see paper) and the second ten structures (11-20) belong to cluster 1 (see paper)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1523D (H)CCH-TOCSY
1633D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1923D F1-[13C]-filtered, F2-[13C]-separated, F3-[15N,13C]-edited NOESY-HSQC
1102F1/F2-[15N,13C]-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] protein, 0.5 mM Glycochenodeoxycholic acid, 0.75 mM glycocholic acid, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-99% 13C; U-99% 15N] protein, 0.5 mM Glycochenodeoxycholic acid, 0.75 mM glycocholic acid, 100% D2O100% D2O
30.5 mM [U-99% 15N] protein, 0.5 mM Glycochenodeoxycholic acid, 0.75 mM Glycocholic acid, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein_1-1[U-99% 13C; U-99% 15N]1
0.5 mMGlycochenodeoxycholic acid-21
0.75 mMglycocholic acid-31
0.5 mMprotein_1-4[U-99% 13C; U-99% 15N]2
0.5 mMGlycochenodeoxycholic acid-52
0.75 mMglycocholic acid-62
0.5 mMprotein_1-7[U-99% 15N]3
0.5 mMGlycochenodeoxycholic acid-83
0.75 mMGlycocholic acid-93
Sample conditionsIonic strength: 30 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker DMXBrukerDMX5002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
HADDOCK2.1Alexandre Bonvinrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: REFINEMENT IN EXPLICIT SOLVENT
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: best HADDOCK score / Conformers calculated total number: 50 / Conformers submitted total number: 20

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