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- PDB-3stm: Structure of human LFABP in complex with one molecule of palmitic acid -

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Basic information

Entry
Database: PDB / ID: 3stm
TitleStructure of human LFABP in complex with one molecule of palmitic acid
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / LFABP / Palmitic acid / Fatty acid binding
Function / homology
Function and homology information


cellular detoxification / Heme degradation / 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 ...cellular detoxification / Heme degradation / 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 / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / 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: 2.216 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.name
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
X: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8562
Polymers14,6001
Non-polymers2561
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.236, 57.392, 74.404
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.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.15 M potassium bromide and 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: May 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.216→28.011 Å / Num. obs: 6817 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 5 % / Rmerge(I) obs: 0.45 / % possible all: 86.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.216→19.176 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.7322 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2805 324 4.79 %
Rwork0.2416 --
obs0.2434 6770 98.86 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.744 Å2 / ksol: 0.278 e/Å3
Displacement parametersBiso max: 69.31 Å2 / Biso mean: 40.3881 Å2 / Biso min: 23.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.8596 Å2-0 Å2-0 Å2
2--0.5958 Å20 Å2
3---0.2638 Å2
Refinement stepCycle: LAST / Resolution: 2.216→19.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 18 66 1065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191009
X-RAY DIFFRACTIONf_angle_d1.2181346
X-RAY DIFFRACTIONf_chiral_restr0.095158
X-RAY DIFFRACTIONf_plane_restr0.004169
X-RAY DIFFRACTIONf_dihedral_angle_d19.081387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2156-2.79010.32091540.291231493303
2.7901-19.17640.26871700.227832973467

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