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- PDB-7fg5: Room temperature structure of the human heart fatty acid-binding ... -

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Basic information

Entry
Database: PDB / ID: 7fg5
TitleRoom temperature structure of the human heart fatty acid-binding protein complexed with capric acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP / complex / binding protein / capric acid / high-strength hydrogel-grown crystal / room temperature structure
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
DECANOIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSugiyama, S. / Kakinouchi, K. / Takahashi, J. / 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: Room temperature structure of the human heart fatty acid-binding protein complexed with capric acid
Authors: Sugiyama, S. / Kakinouchi, K. / Takahashi, J. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
History
DepositionJul 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 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)15,0512
Polymers14,8791
Non-polymers1721
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.147, 70.948, 34.511
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-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl (pH8.5), 55% PEG 400

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 33797 / % possible obs: 98.9 % / Redundancy: 7.1 % / Rpim(I) all: 0.03 / Net I/σ(I): 9.4
Reflection shellResolution: 1.3→1.32 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1532 / Rpim(I) all: 0.267

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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: 4TJZ

4tjz


Resolution: 1.3→43.54 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.257 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1784 1715 5.1 %RANDOM
Rwork0.14722 ---
obs0.14884 32033 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.509 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2---0.54 Å20 Å2
3----1.08 Å2
Refinement stepCycle: 1 / Resolution: 1.3→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 12 132 1185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131264
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171211
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.661730
X-RAY DIFFRACTIONr_angle_other_deg1.4721.6172833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.955170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.42424.21157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26315242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.782155
X-RAY DIFFRACTIONr_chiral_restr0.1020.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02249
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_it1.891.314635
X-RAY DIFFRACTIONr_mcbond_other1.8441.311634
X-RAY DIFFRACTIONr_mcangle_it2.4421.991820
X-RAY DIFFRACTIONr_mcangle_other2.4411.995821
X-RAY DIFFRACTIONr_scbond_it3.0621.785629
X-RAY DIFFRACTIONr_scbond_other3.061.787630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3632.5911
X-RAY DIFFRACTIONr_long_range_B_refined3.82916.9461305
X-RAY DIFFRACTIONr_long_range_B_other3.63916.3571277
X-RAY DIFFRACTIONr_rigid_bond_restr6.29632475
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.333 Å
RfactorNum. reflection% reflection
Rfree0.332 94 -
Rwork0.269 2167 -
obs--90.91 %

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