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- PDB-7fd7: The 1.00 angstrom X-ray structure of the human heart fatty acid-b... -

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Basic information

Entry
Database: PDB / ID: 7fd7
TitleThe 1.00 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with perfluoroheptanoic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP / Complex / Binding protein / perfluoroheptanoic 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
perfluoroheptanoic acid / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsSugiyama, S. / Kakinouchi, K. / Hara, T. / Nakano, R. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJTM19DC Japan
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
Japan Science and TechnologyJPMJER1005 Japan
Other private09-003-005 Japan
CitationJournal: To Be Published
Title: The 1.00 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with perfluoroheptanoic acid
Authors: Sugiyama, S. / Kakinouchi, K. / Hara, T. / Nakano, R. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
History
DepositionJul 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,8454
Polymers14,8791
Non-polymers9663
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-0 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.829, 69.493, 33.881
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-4EI / perfluoroheptanoic acid


Mass: 364.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7HF13O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl (pH 8.0 or 8.5), 55% 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: 1→50 Å / Num. obs: 68057 / % possible obs: 96.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.3
Reflection shellResolution: 1→1.02 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2960

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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: 1→28.84 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.666 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.147 3451 5.1 %RANDOM
Rwork0.12203 ---
obs0.12335 64502 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å20 Å2
2--1.11 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 1→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 60 220 1321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0131363
X-RAY DIFFRACTIONr_bond_other_d0.0050.0171258
X-RAY DIFFRACTIONr_angle_refined_deg2.3371.7171885
X-RAY DIFFRACTIONr_angle_other_deg1.571.622951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69524.42661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36115255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.275155
X-RAY DIFFRACTIONr_chiral_restr0.1090.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021551
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02264
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_it2.7871.158659
X-RAY DIFFRACTIONr_mcbond_other1.8641.147658
X-RAY DIFFRACTIONr_mcangle_it2.7731.743857
X-RAY DIFFRACTIONr_mcangle_other3.0731.752858
X-RAY DIFFRACTIONr_scbond_it5.8461.573704
X-RAY DIFFRACTIONr_scbond_other5.8461.573704
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7692.2981029
X-RAY DIFFRACTIONr_long_range_B_refined5.97918.2931607
X-RAY DIFFRACTIONr_long_range_B_other5.26316.7211523
X-RAY DIFFRACTIONr_rigid_bond_restr12.49732621
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 214 -
Rwork0.222 4083 -
obs--83.4 %

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