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- PDB-1b56: HUMAN RECOMBINANT EPIDERMAL FATTY ACID BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1b56
TitleHUMAN RECOMBINANT EPIDERMAL FATTY ACID BINDING PROTEIN
ComponentsFATTY ACID BINDING PROTEINFatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING / FATTY ACID TRANSPORT / BETA BARREL
Function / homology
Function and homology information


regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity / Triglyceride catabolism / epidermis development / fatty acid transport / long-chain fatty acid transport / secretory granule membrane / fatty acid binding / lipid metabolic process / glucose metabolic process / azurophil granule lumen / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / synapse / lipid binding / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsVan Tilbeurgh, H. / Hohoff, C. / Borchers, T. / Spener, F.
CitationJournal: Biochemistry / Year: 1999
Title: Expression, purification, and crystal structure determination of recombinant human epidermal-type fatty acid binding protein.
Authors: Hohoff, C. / Borchers, T. / Rustow, B. / Spener, F. / van Tilbeurgh, H.
History
DepositionJan 12, 1999Processing site: BNL
Revision 1.0Oct 5, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4422
Polymers15,1851
Non-polymers2561
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.450, 63.450, 76.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein FATTY ACID BINDING PROTEIN / Fatty acid-binding protein


Mass: 15185.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: EPIDERMIS / Production host: Escherichia coli (E. coli) / References: UniProt: Q01469
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.55 Å3/Da / Density % sol: 52 %
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1reservoir
20.2 Msodium potassium tartrate1reservoir
30.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 10321 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 12 / % possible all: 100
Reflection
*PLUS
Num. measured all: 72226 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HMB

2hmb


Resolution: 2.05→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: PROBABLY ALTERNATIVE CONFORMATIONS FOR THE LOOP BETWEEN RESIDUES 59 AND 62 N TERMINAL REGION DISORDERED NATURE OF THE BOUND LIGAND NOT CERTAIN COULD BE A MIXTURE OF LIGANDS, NO EXTRA LIGAND ...Details: PROBABLY ALTERNATIVE CONFORMATIONS FOR THE LOOP BETWEEN RESIDUES 59 AND 62 N TERMINAL REGION DISORDERED NATURE OF THE BOUND LIGAND NOT CERTAIN COULD BE A MIXTURE OF LIGANDS, NO EXTRA LIGAND WAS USED IN THE CRYSTALLIZATION LIQUOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 -10 %RANDOM
Rwork0.207 ---
obs0.207 9509 99.9 %-
Displacement parametersBiso mean: 28.2 Å2
Refinement stepCycle: LAST / Resolution: 2.05→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 18 51 1170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.265
Solvent computation
*PLUS
Displacement parameters
*PLUS

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