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- PDB-2f73: Crystal structure of human fatty acid binding protein 1 (FABP1) -

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Basic information

Entry
Database: PDB / ID: 2f73
TitleCrystal structure of human fatty acid binding protein 1 (FABP1)
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / fatty acid binding protein / Structural Genomics / Structural Genomics Consortium / SGC
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKursula, P. / Thorsell, A.G. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Holmberg Schiavone, L. ...Kursula, P. / Thorsell, A.G. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Holmberg Schiavone, L. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / van den Berg, S. / Weigelt, J. / Hallberg, B.M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human FABP1
Authors: Kursula, P. / Thorsell, A.G. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Holmberg Schiavone, L. / Kotenyova, T. / Nilsson-Ehle, P. ...Authors: Kursula, P. / Thorsell, A.G. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Holmberg Schiavone, L. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / van den Berg, S. / Weigelt, J. / Hallberg, B.M. / Structural Genomics Consortium (SGC)
History
DepositionNov 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver
B: Fatty acid-binding protein, liver
C: Fatty acid-binding protein, liver
D: Fatty acid-binding protein, liver
E: Fatty acid-binding protein, liver
F: Fatty acid-binding protein, liver
G: Fatty acid-binding protein, liver
H: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)134,2818
Polymers134,2818
Non-polymers00
Water72140
1
A: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)16,7851
Polymers16,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)16,7851
Polymers16,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)16,7851
Polymers16,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)16,7851
Polymers16,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)16,7851
Polymers16,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)16,7851
Polymers16,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)16,7851
Polymers16,7851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)16,7851
Polymers16,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.052, 78.134, 235.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16785.117 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Production host: Escherichia coli (E. coli) / References: UniProt: P07148
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9781 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 49103 / Num. obs: 49103 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 50 Å2 / Rsym value: 0.084 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 5391 / Rsym value: 0.655 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LFO

1lfo


Resolution: 2.5→20 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
Details: The twinning operator k,h,-l and the twinning fraction 0.27 were used in the refinement. THis is pseudomerohedral twinning.
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 2088 -Test reflections were selected such that they are not related to the working set via the twinning operator
Rwork0.2503 ---
all-48193 --
obs-48193 99.6 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8536 0 0 40 8576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.61
X-RAY DIFFRACTIONc_mcangle_it2.81

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