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- PDB-3stn: Structure of human LFABP (apo-LFABP) -

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Basic information

Entry
Database: PDB / ID: 3stn
TitleStructure of human LFABP (apo-LFABP)
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / LFABP / Palmitic acid / Fatty acid binding
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.595 Å
AuthorsSharma, A. / Sharma, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Fatty acid induced remodeling within the Human liver fatty acid binding protein
Authors: Sharma, A. / Sharma, A.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,6001
Polymers14,6001
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.135, 57.080, 74.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 14599.728 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) / References: UniProt: P07148
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.15M potassium bromide, 30% polyethylene glycol monomethyl ether (PEG MME) 2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 4305 / Num. obs: 4274 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.43 / % possible all: 92.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.595→9.979 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.7322 / SU ML: 0 / σ(F): 0.65 / Phase error: 30.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 188 4.52 %
Rwork0.2447 --
obs0.2465 4163 99.24 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.797 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso max: 160.35 Å2 / Biso mean: 65.6299 Å2 / Biso min: 25.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.595→9.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 0 0 14 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031011
X-RAY DIFFRACTIONf_angle_d0.2221356
X-RAY DIFFRACTIONf_chiral_restr0.016159
X-RAY DIFFRACTIONf_plane_restr0.001173
X-RAY DIFFRACTIONf_dihedral_angle_d23.857382
LS refinement shellResolution: 2.5945→9.9795 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2667 188 -
Rwork0.2447 3975 -
all-4163 -
obs--99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8827-0.1832-0.03741.8681-0.1750.01720.19850.25310.29920.0659-0.3004-0.0580.03720.06410.12170.43730.1260.06430.4776-0.01830.36637.50510.2165-14.5232
20.74520.9929-0.0521.347-0.12640.89070.2420.04550.0686-0.11750.10270.80830.45740.2021-0.27420.43030.1469-0.23440.28420.01770.35473.5403-8.1672-19.4884
31.0966-0.99041.3791.1412-1.62142.48030.1082-0.1586-0.3049-0.24940.38810.71310.3932-0.2408-0.50140.334-0.1-0.00490.33310.02330.55491.5064-15.9402-11.9143
40.7180.6096-0.62360.94080.22281.81970.1406-0.0006-0.1530.0098-0.1769-0.3784-0.18090.47570.07370.2062-0.0001-0.00310.3650.06730.27613.1042-8.1445-14.0282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:13)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 14:54)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 55:82)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 83:127)A0

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