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- PDB-7wdj: The 0.90 angstrom X-ray structure of the human heart fatty acid-b... -

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Basic information

Entry
Database: PDB / ID: 7wdj
TitleThe 0.90 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with linoleic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP3 / complex / binding protein / linoleic 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 protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
LINOLEIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsSugiyama, S. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJTM19DC Japan
Japan Science and TechnologyJPMJER1005 Japan
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
Other private09-003-005 Japan
CitationJournal: To Be Published
Title: The 0.90 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with linoleic acid
Authors: Sugiyama, S. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
History
DepositionDec 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,7244
Polymers14,8791
Non-polymers8453
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-2 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.620, 69.733, 33.617
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-EIC / LINOLEIC ACID / 9,12-LINOLEIC ACID


Mass: 280.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / 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.: 148 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Hepes-NaOH (pH7.5), 60% PEG 400 or 0.1M Glycine-NaOH (pH9.0), 60% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.75 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 0.9→43 Å / Num. obs: 95206 / % possible obs: 99.5 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.1
Reflection shellResolution: 0.9→0.92 Å / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4699

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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: 0.9→30.3 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.357 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12647 4773 5 %RANDOM
Rwork0.11863 ---
obs0.11902 90365 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 0.9→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 40 148 1227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131286
X-RAY DIFFRACTIONr_bond_other_d0.0040.0181257
X-RAY DIFFRACTIONr_angle_refined_deg2.2981.6921739
X-RAY DIFFRACTIONr_angle_other_deg1.6561.6892950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.46324.6354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0215241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.962154
X-RAY DIFFRACTIONr_chiral_restr0.110.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021454
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02250
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_it5.7830.833623
X-RAY DIFFRACTIONr_mcbond_other5.7560.823622
X-RAY DIFFRACTIONr_mcangle_it5.0861.214805
X-RAY DIFFRACTIONr_mcangle_other5.1041.223806
X-RAY DIFFRACTIONr_scbond_it7.0341.231663
X-RAY DIFFRACTIONr_scbond_other7.0161.235663
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1881.667935
X-RAY DIFFRACTIONr_long_range_B_refined7.17910.831364
X-RAY DIFFRACTIONr_long_range_B_other6.99610.5671338
X-RAY DIFFRACTIONr_rigid_bond_restr11.73332541
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.9→0.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 355 -
Rwork0.219 6581 -
obs--99.18 %

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