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- PDB-7wkg: The 0.84 angstrom X-ray structure of the human heart fatty acid-b... -

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Basic information

Entry
Database: PDB / ID: 7wkg
TitleThe 0.84 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with erucic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP3 / complex / binding protein / erucic acid / cis-13-docosenoic 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 / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
(Z)-docos-13-enoic acid / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.84 Å
AuthorsSugiyama, S. / Kakinouchi, K. / Nakano, R. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
Funding support4items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJTM19DC
Japan Science and TechnologyJPMJER1005
Japan Society for the Promotion of Science (JSPS)19K06588
Other private09-003-005
CitationJournal: To Be Published
Title: The 0.84 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with erucic acid
Authors: Sugiyama, S. / Kakinouchi, K. / Nakano, R. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
History
DepositionJan 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,5003
Polymers14,8791
Non-polymers6212
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-1 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.653, 69.895, 33.986
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: 14879.022 Da / Num. of mol.: 1
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-08O / (Z)-docos-13-enoic acid


Mass: 338.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H42O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl (pH8.0), 50% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.84→43.05 Å / Num. obs: 118460 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.4
Reflection shellResolution: 0.84→0.85 Å / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 2 / Num. unique obs: 5885

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WVM

3wvm


Resolution: 0.84→22.26 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.282 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.11934 5937 5 %RANDOM
Rwork0.1053 ---
obs0.10599 112439 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.086 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2--0.19 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 0.84→22.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 43 229 1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131513
X-RAY DIFFRACTIONr_bond_other_d0.0060.0181517
X-RAY DIFFRACTIONr_angle_refined_deg2.6211.6932052
X-RAY DIFFRACTIONr_angle_other_deg1.6851.7083574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6985198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.60223.84665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59615292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.679156
X-RAY DIFFRACTIONr_chiral_restr0.1060.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021699
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02295
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1280.657726
X-RAY DIFFRACTIONr_mcbond_other2.1250.656725
X-RAY DIFFRACTIONr_mcangle_it2.2010.986946
X-RAY DIFFRACTIONr_mcangle_other2.2010.987947
X-RAY DIFFRACTIONr_scbond_it3.2650.906787
X-RAY DIFFRACTIONr_scbond_other3.2630.906788
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2491.2731107
X-RAY DIFFRACTIONr_long_range_B_refined4.51310.0071913
X-RAY DIFFRACTIONr_long_range_B_other3.9559.211835
X-RAY DIFFRACTIONr_rigid_bond_restr22.15533030
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.84→0.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 450 -
Rwork0.2 8163 -
obs--99.1 %

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