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- PDB-4lkp: Crystal Structure of Apo Human Epidermal Fatty Acid Binding Prote... -

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Basic information

Entry
Database: PDB / ID: 4lkp
TitleCrystal Structure of Apo Human Epidermal Fatty Acid Binding Protein (FABP5)
ComponentsFatty acid-binding protein, epidermal
KeywordsLIPID BINDING PROTEIN / Beta Barrel / Beta Clam / Fatty Acid Binding Protein / Fatty Acids / Nucleus
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 D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / 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 D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / long-chain fatty acid transmembrane transporter activity / Signaling by Retinoic Acid / Triglyceride catabolism / epidermis development / long-chain fatty acid transport / fatty acid transport / secretory granule membrane / fatty acid binding / lipid metabolic process / glucose metabolic process / azurophil granule lumen / positive regulation of cold-induced thermogenesis / glucose homeostasis / postsynaptic density / lipid binding / Neutrophil degranulation / synapse / 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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
AMMONIUM ION / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsArmstrong, E.H. / Ortlund, E.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural basis for ligand regulation of the fatty acid-binding protein 5, peroxisome proliferator-activated receptor beta / delta (FABP5-PPAR beta / delta ) signaling pathway.
Authors: Armstrong, E.H. / Goswami, D. / Griffin, P.R. / Noy, N. / Ortlund, E.A.
History
DepositionJul 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7646
Polymers15,4581
Non-polymers3065
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.971, 62.971, 74.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fatty acid-binding protein, epidermal / Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein 5 / Psoriasis- ...Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein 5 / Psoriasis-associated fatty acid-binding protein homolog / PA-FABP


Mass: 15457.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP5 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01469

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Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0M ammonium sulfate, 300mM Na/K tartrate, 100mM Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 18056 / Num. obs: 18056 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.042 / Χ2: 1.113 / Net I/σ(I): 21.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.67-1.736.80.38917441.178199.4
1.73-1.88.70.27517771.209199.8
1.8-1.889.40.19817701.1531100
1.88-1.989.60.12517481.1771100
1.98-2.19.60.09317971.2231100
2.1-2.279.60.07417771.231100
2.27-2.499.50.05418101.1531100
2.49-2.869.50.04218141.0921100
2.86-3.69.40.02918410.966199.9
3.6-508.80.02419780.789199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.8 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.09 Å
Translation2.5 Å48.09 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→48.092 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.858 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 20.29 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 918 5.1 %Random
Rwork0.181 ---
obs0.1826 18008 99.92 %-
all-18034 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.63 Å2 / Biso mean: 20.9284 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: LAST / Resolution: 1.67→48.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 15 111 1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151128
X-RAY DIFFRACTIONf_angle_d1.8251528
X-RAY DIFFRACTIONf_chiral_restr0.127178
X-RAY DIFFRACTIONf_plane_restr0.008193
X-RAY DIFFRACTIONf_dihedral_angle_d15.595440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.67-1.75740.31271280.2345238225102510
1.7574-1.86750.24761460.2071236325092509
1.8675-2.01170.23191410.1791239625372537
2.0117-2.21410.22081500.1729239425442544
2.2141-2.53450.20951200.1774244225622562
2.5345-3.19310.22531100.1939248425942594
3.1931-48.11210.1871230.1686262927522752

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