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- PDB-1fe3: CRYSTAL STRUCTURE OF HUMAN BRAIN FATTY ACID BINDING PROTEIN OLEIC ACID -

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Basic information

Entry
Database: PDB / ID: 1fe3
TitleCRYSTAL STRUCTURE OF HUMAN BRAIN FATTY ACID BINDING PROTEIN OLEIC ACID
ComponentsFATTY ACID-BINDING PROTEIN, BRAIN
KeywordsLIPID BINDING PROTEIN / OA / BLBP / LIPID-BINDING PROTEIN
Function / homology
Function and homology information


NOTCH3 Intracellular Domain Regulates Transcription / Triglyceride catabolism / fatty acid transport / epithelial cell proliferation / fatty acid binding / nervous system development / negative regulation of cell population proliferation / lipid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / Fatty acid-binding protein, brain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBalendiran, G.K.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure and thermodynamic analysis of human brain fatty acid-binding protein.
Authors: Balendiran, G.K. / Schnutgen, F. / Scapin, G. / Borchers, T. / Xhong, N. / Lim, K. / Godbout, R. / Spener, F. / Sacchettini, J.C.
History
DepositionJul 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: FATTY ACID-BINDING PROTEIN, BRAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0592
Polymers14,7771
Non-polymers2821
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.60, 93.60, 46.70
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

#1: Protein FATTY ACID-BINDING PROTEIN, BRAIN / BRAIN LIPID-BINDING PROTEIN


Mass: 14776.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15540
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2

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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: 4 Å3/Da / Density % sol: 69.22 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8-2.2 Mammonium sulfate1reservoir
2100 mMTris1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 11489 / Num. obs: 11489 / % possible obs: 82.5 % / Rsym value: 0.072
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 5444 / Num. measured all: 11489 / Rmerge(I) obs: 0.072

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→15 Å
RfactorNum. reflection
Rfree0.279 -
Rwork0.261 -
all0.261 -
obs-5444
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 20 0 1057
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

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