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- PDB-3wvm: The 0.88 angstrom X-ray structure of the human heart fatty acid-b... -

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Basic information

Entry
Database: PDB / ID: 3wvm
TitleThe 0.88 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with stearic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / antiparallel beta barrel
Function / homology
Function and homology information


icosatetraenoic acid binding / positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / oleic acid binding / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / response to fatty acid / phospholipid homeostasis / long-chain fatty acid transmembrane transporter activity ...icosatetraenoic acid binding / positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / oleic acid binding / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / response to fatty acid / phospholipid homeostasis / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / Triglyceride catabolism / sarcoplasm / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / fatty acid metabolic process / response to insulin / response to xenobiotic stimulus / 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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
STEARIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.88 Å
AuthorsSugiyama, S. / Matsuoka, S. / Mizohata, E. / Matsuoka, D. / Ishida, H. / Hirose, M. / Kakinouchi, K. / Hara, T. / Matsumura, H. / Murakami, S. ...Sugiyama, S. / Matsuoka, S. / Mizohata, E. / Matsuoka, D. / Ishida, H. / Hirose, M. / Kakinouchi, K. / Hara, T. / Matsumura, H. / Murakami, S. / Inoue, T. / Murata, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Water-mediated recognition of simple alkyl chains by heart-type fatty-acid-binding protein.
Authors: Matsuoka, S. / Sugiyama, S. / Matsuoka, D. / Hirose, M. / Lethu, S. / Ano, H. / Hara, T. / Ichihara, O. / Kimura, S.R. / Murakami, S. / Ishida, H. / Mizohata, E. / Inoue, T. / Murata, M.
History
DepositionMay 25, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)15,7284
Polymers14,8791
Non-polymers8493
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.557, 69.418, 33.812
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 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05413
#2: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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 / pH: 8.5
Details: 55%(v/v) PEG400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 12, 2013
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.88→50 Å / Num. all: 102203 / Num. obs: 100773 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.4 % / Rmerge(I) obs: 0.066
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
0.88-0.96.60.4232.454408187
0.9-0.917.70.3974805195.3
0.91-0.9310.10.3724966198.4
0.93-0.9511.50.3314972198.9
0.95-0.9711.70.2895017199.1
0.97-0.9911.90.2515039199

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Processing

Software
NameVersionClassification
BSSdata collection
CCP4model building
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.88→42.89 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.305 / SU ML: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0 / 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
Rfree0.11267 5025 5 %RANDOM
Rwork0.10765 ---
all0.1079 95629 --
obs0.1079 95629 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.508 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.03 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 0.88→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 55 174 1273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191377
X-RAY DIFFRACTIONr_bond_other_d0.0040.021368
X-RAY DIFFRACTIONr_angle_refined_deg2.3851.981870
X-RAY DIFFRACTIONr_angle_other_deg1.1333198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.135183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.51225.27355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22915263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.043156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021578
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02288
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_it1.470.65669
X-RAY DIFFRACTIONr_mcbond_other1.3420.644668
X-RAY DIFFRACTIONr_mcangle_it1.8190.978873
X-RAY DIFFRACTIONr_mcangle_other1.8560.982874
X-RAY DIFFRACTIONr_scbond_it2.7480.949708
X-RAY DIFFRACTIONr_scbond_other2.7470.953709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1111.308998
X-RAY DIFFRACTIONr_long_range_B_refined3.5416.971702
X-RAY DIFFRACTIONr_long_range_B_other3.3336.4291600
X-RAY DIFFRACTIONr_rigid_bond_restr7.39232745
X-RAY DIFFRACTIONr_sphericity_free18.983540
X-RAY DIFFRACTIONr_sphericity_bonded7.70352858
LS refinement shellResolution: 0.881→0.904 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 308 -
Rwork0.192 6369 -
obs--89.35 %

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