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- PDB-5b29: The 1.28A structure of human FABP3 F16V mutant complexed with pal... -

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Basic information

Entry
Database: PDB / ID: 5b29
TitleThe 1.28A structure of human FABP3 F16V mutant complexed with palmitic acid at room temperature
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / complex / palmitic acid
Function / homology
Function and homology information


positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport ...positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / negative regulation of cell population proliferation / extracellular space / extracellular exosome / nucleus / cytosol
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
PALMITIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.28 Å
AuthorsMatsuoka, D. / Sugiyama, S. / Kakinouchi, K. / Niiyama, M. / Murata, M. / Matsuoka, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
JSPS KAKENHI24681045 Japan
JSPS KAKENHI26560436 Japan
JSPS KAKENHI25650051 Japan
JSPS KAKENHI25286051 Japan
CitationJournal: To Be Published
Title: The 1.28A structure of human FABP3 F16V mutant complexed with palmitic acid at room temperature.
Authors: Matsuoka, D. / Sugiyama, S. / Kakinouchi, K. / Niiyama, M. / Murata, M. / Matsuoka, S.
History
DepositionJan 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9562
Polymers14,7001
Non-polymers2561
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint1 kcal/mol
Surface area7150 Å2
Unit cell
Length a, b, c (Å)55.220, 71.018, 34.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein, heart / Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived ...Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived growth inhibitor / MDGI / Muscle fatty acid-binding protein / M-FABP


Mass: 14699.782 Da / Num. of mol.: 1 / Mutation: F16V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli (E. coli) / References: UniProt: P05413
#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.: 131 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl (pH8.0), 45-55% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.28→31.07 Å / Num. obs: 35762 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.6
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.28→31.07 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 1786 5 %
Rwork0.161 --
obs0.163 35707 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.28→31.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 18 131 1181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091227
X-RAY DIFFRACTIONf_angle_d1.0141678
X-RAY DIFFRACTIONf_dihedral_angle_d16.671487
X-RAY DIFFRACTIONf_chiral_restr0.093204
X-RAY DIFFRACTIONf_plane_restr0.005210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2794-1.3140.35371320.31892508X-RAY DIFFRACTION98
1.314-1.35260.45811230.33882585X-RAY DIFFRACTION100
1.3526-1.39630.44061170.37412615X-RAY DIFFRACTION100
1.3963-1.44620.50411340.41242588X-RAY DIFFRACTION100
1.4462-1.50410.41951500.35512573X-RAY DIFFRACTION100
1.5041-1.57250.35491360.27692584X-RAY DIFFRACTION100
1.5725-1.65540.20821530.16922564X-RAY DIFFRACTION100
1.6554-1.75910.16351350.11272605X-RAY DIFFRACTION100
1.7591-1.8950.17851260.10412624X-RAY DIFFRACTION100
1.895-2.08560.13381540.09762599X-RAY DIFFRACTION100
2.0856-2.38730.13821340.11212651X-RAY DIFFRACTION100
2.3873-3.00740.17181460.14392666X-RAY DIFFRACTION100
3.0074-31.08120.18161460.1482759X-RAY DIFFRACTION98

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