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- PDB-2l67: Solution Structure of Human Apo L-FABP -

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Basic information

Entry
Database: PDB / ID: 2l67
TitleSolution Structure of Human Apo L-FABP
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / fatty acid carrier / apo form
Function / homology
Function and homology information


response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / phospholipid binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PPARA activates gene expression / Cytoprotection by HMOX1 / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / nucleoplasm / 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
Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsfewest violations, model 1
AuthorsCai, J. / Luecke, C. / Chen, Z. / Qiao, Y. / Klimtchuk, E.S. / Hamilton, J.A.
CitationJournal: Biophys.J. / Year: 2012
Title: Solution structure and backbone dynamics of human liver fatty acid binding protein: fatty acid binding revisited.
Authors: Cai, J. / Lucke, C. / Chen, Z. / Qiao, Y. / Klimtchuk, E. / Hamilton, J.A.
History
DepositionNov 17, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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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)14,0951
Polymers14,0951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver-type fatty acid-binding protein / L-FABP


Mass: 14095.169 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Production host: Escherichia coli (E. coli) / Strain (production host): MG1655 / References: UniProt: P07148

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1423D 1H-15N NOESY
1523D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM potassium phosphate, 150 mM sodium chloride, 0.05 % sodium azide, 2-3 mM human liver fatty acid binding protein, 95% H2O/5% D2O95% H2O/5% D2O
220 mM potassium phosphate, 150 mM sodium chloride, 0.05 % sodium azide, 2-3 mM [U-15N] human liver fatty acid binding protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
20 mMpotassium phosphate-11
150 mMsodium chloride-21
0.05 %sodium azide-31
mMhuman liver fatty acid binding protein-42-31
20 mMpotassium phosphate-52
150 mMsodium chloride-62
0.05 %sodium azide-72
mMhuman liver fatty acid binding protein-8[U-15N]2-32
Sample conditionsIonic strength: 150 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Discover2000Accelrys Software Inc.refinement
NMRView8Johnson, One Moon Scientificdata analysis
NMRView8Johnson, One Moon Scientificpeak picking
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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