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- PDB-3stk: Crystal Structure of human LFABP complex with two molecules of pa... -

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Basic information

Entry
Database: PDB / ID: 3stk
TitleCrystal Structure of human LFABP complex with two molecules of palmitic acid (holo-LFABP)
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / LFABP / Palmitic acid / Fatty acid binding
Function / homology
Function and homology information


oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / cellular detoxification / response to vitamin B3 / long-chain fatty acid transmembrane transporter activity / Heme degradation / heterocyclic compound binding ...oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / cellular detoxification / response to vitamin B3 / long-chain fatty acid transmembrane transporter activity / Heme degradation / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / 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
PALMITIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)15,1133
Polymers14,6001
Non-polymers5132
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.283, 57.097, 74.861
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: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.22 Å3/Da / Density % sol: 44.51 % / Mosaicity: 1.716 °
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 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 18383 / % possible obs: 92.2 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.046 / Χ2: 1.978 / Net I/σ(I): 24
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.54-1.69.90.38514141.247171.8
1.6-1.6611.40.27718041.361193
1.66-1.7311.50.20218141.468193.3
1.73-1.8311.30.13518491.79194.5
1.83-1.9410.40.09718552.178194.4
1.94-2.0910.80.06418972.157195.8
2.09-2.39.90.05419022.47195.4
2.3-2.6310.80.0419301.948197.2
2.63-3.3211.40.03720092.159198.3
3.32-509.50.04319092.945188.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→25.193 Å / Occupancy max: 1 / Occupancy min: 0.89 / FOM work R set: 0.8738 / SU ML: 0.41 / σ(F): 1.33 / Phase error: 19.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 934 5.13 %
Rwork0.2073 --
obs0.2084 18190 93.13 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.979 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 54.52 Å2 / Biso mean: 25.135 Å2 / Biso min: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.2947 Å20 Å2-0 Å2
2--0.0629 Å20 Å2
3----0.3577 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 36 224 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061046
X-RAY DIFFRACTIONf_angle_d1.0221388
X-RAY DIFFRACTIONf_chiral_restr0.066159
X-RAY DIFFRACTIONf_plane_restr0.003174
X-RAY DIFFRACTIONf_dihedral_angle_d16.677412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5502-1.63190.46591420.41962289243189
1.6319-1.73410.3631400.32452404254493
1.7341-1.8680.28541420.22242448259094
1.868-2.05590.23191210.2052456257794
2.0559-2.35320.20591270.20062510263794
2.3532-2.9640.25751430.19712603274698
2.964-25.1960.18481190.1912546266590

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