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- PDB-4tkh: The 0.93 angstrom X-ray structure of the human heart fatty acid-b... -

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Basic information

Entry
Database: PDB / ID: 4tkh
TitleThe 0.93 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with myristic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / antiparallel beta barrel / fatty acid-binding protein / human heart / myristic acid
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
MYRISTIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.93 Å
AuthorsSugiyama, S. / Matsuoka, S. / Mizohata, E. / Matsuoka, D. / Ishida, H. / Hirose, M. / Kakinouchi, K. / Hara, T. / Murakami, S. / Inoue, T. / Murata, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSP ERATO Japan
JSPS KAKENHI25286051 Japan
JSPS KAKENHI25650051 Japan
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 26, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Jan 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,3903
Polymers14,8791
Non-polymers5112
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint2 kcal/mol
Surface area7270 Å2
Unit cell
Length a, b, c (Å)54.568, 69.475, 33.835
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 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05413
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl, 55%(v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.93→50 Å / Num. obs: 86123 / % possible obs: 98.9 % / Redundancy: 11.6 % / Net I/σ(I): 10.1
Reflection shellResolution: 0.93→0.95 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.49 / % possible all: 97.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.93→42.91 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.416 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12559 4309 5 %RANDOM
Rwork0.11523 ---
obs0.11575 81538 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.706 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.02 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 0.93→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 35 165 1244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191297
X-RAY DIFFRACTIONr_bond_other_d0.0020.021296
X-RAY DIFFRACTIONr_angle_refined_deg2.3111.9931759
X-RAY DIFFRACTIONr_angle_other_deg0.96533026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.54625.4951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63815257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.282155
X-RAY DIFFRACTIONr_chiral_restr0.1180.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021473
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02266
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_it1.60.816636
X-RAY DIFFRACTIONr_mcbond_other1.5730.814635
X-RAY DIFFRACTIONr_mcangle_it1.8871.231823
X-RAY DIFFRACTIONr_mcangle_other1.91.233824
X-RAY DIFFRACTIONr_scbond_it4.2361.178661
X-RAY DIFFRACTIONr_scbond_other4.2341.177662
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7461.617937
X-RAY DIFFRACTIONr_long_range_B_refined3.7398.0221529
X-RAY DIFFRACTIONr_long_range_B_other3.5427.4391438
X-RAY DIFFRACTIONr_rigid_bond_restr9.24332593
X-RAY DIFFRACTIONr_sphericity_free23.262540
X-RAY DIFFRACTIONr_sphericity_bonded9.05952703
LS refinement shellResolution: 0.93→0.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 297 -
Rwork0.215 5886 -
obs--97.54 %

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