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- PDB-7fdt: The 0.86 angstrom X-ray structure of the human heart fatty acid-b... -

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Basic information

Entry
Database: PDB / ID: 7fdt
TitleThe 0.86 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with elaidic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP / Complex / Binding protein / elaidic 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
9-OCTADECENOIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 Å
AuthorsSugiyama, S. / Kakinouchi, K. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJTM19DC Japan
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
Japan Science and TechnologyJPMJER1005 Japan
CitationJournal: To Be Published
Title: The 0.86 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with octanoic acid
Authors: Sugiyama, S. / Kakinouchi, K. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
History
DepositionJul 17, 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)15,4443
Polymers14,8791
Non-polymers5652
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-1 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.572, 69.973, 33.906
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-ELA / 9-OCTADECENOIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / 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.: 206 / 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: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl (pH8.5), 50% 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: 0.8 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.86→50 Å / Num. obs: 108729 / % possible obs: 98.1 % / Redundancy: 10.9 % / Rpim(I) all: 0.023 / Net I/σ(I): 14.6
Reflection shellResolution: 0.86→0.87 Å / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4463 / Rpim(I) all: 0.163

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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: 0.86→28.82 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.257 / SU ML: 0.007 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1205 5448 5 %RANDOM
Rwork0.11286 ---
obs0.11324 103069 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.167 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 0.86→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 39 206 1286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0131331
X-RAY DIFFRACTIONr_bond_other_d0.0050.0181316
X-RAY DIFFRACTIONr_angle_refined_deg2.4871.6941800
X-RAY DIFFRACTIONr_angle_other_deg1.6311.6973090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.65324.03557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15115255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.376155
X-RAY DIFFRACTIONr_chiral_restr0.120.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021502
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02261
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_it1.8520.606641
X-RAY DIFFRACTIONr_mcbond_other1.8370.605640
X-RAY DIFFRACTIONr_mcangle_it1.9310.917831
X-RAY DIFFRACTIONr_mcangle_other1.9350.918832
X-RAY DIFFRACTIONr_scbond_it4.3080.943690
X-RAY DIFFRACTIONr_scbond_other4.3050.942691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9381.276970
X-RAY DIFFRACTIONr_long_range_B_refined3.999.1251461
X-RAY DIFFRACTIONr_long_range_B_other3.7378.5121410
X-RAY DIFFRACTIONr_rigid_bond_restr12.53532647
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.86→0.882 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 331 -
Rwork0.202 6398 -
obs--82.92 %

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