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- PDB-4tkj: The 0.87 angstrom X-ray structure of the human heart fatty acid-b... -

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Basic information

Entry
Database: PDB / ID: 4tkj
TitleThe 0.87 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with palmitic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / antiparallel beta barrel / fatty acid-binding protein / human heart / palmitic 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-GLP / PALMITIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.87 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
JST ERATO1859 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 / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_assembly_prop / 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.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,9595
Polymers14,8791
Non-polymers1,0804
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-1 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.706, 69.894, 33.655
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 BL21(DE3) (bacteria) / References: UniProt: P05413
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#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: Sugar ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P
IdentifierTypeProgram
a-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.87→50 Å / Num. obs: 106214 / % possible obs: 99.5 % / Redundancy: 9.6 % / Net I/σ(I): 10.3
Reflection shellResolution: 0.87→0.89 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.87→43.08 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.285 / SU ML: 0.008 / 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
Rfree0.12064 5281 5 %RANDOM
Rwork0.10931 ---
obs0.10988 100656 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.346 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2---0 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 0.87→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 66 189 1299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191393
X-RAY DIFFRACTIONr_bond_other_d0.0050.021395
X-RAY DIFFRACTIONr_angle_refined_deg2.5122.0141893
X-RAY DIFFRACTIONr_angle_other_deg1.35833264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.62526.03853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.149154
X-RAY DIFFRACTIONr_chiral_restr0.1860.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021574
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02280
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_it1.0560.657672
X-RAY DIFFRACTIONr_mcbond_other1.0580.656670
X-RAY DIFFRACTIONr_mcangle_it1.3060.995875
X-RAY DIFFRACTIONr_mcangle_other1.3070.996876
X-RAY DIFFRACTIONr_scbond_it2.6450.944721
X-RAY DIFFRACTIONr_scbond_other2.6330.943721
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9591.311019
X-RAY DIFFRACTIONr_long_range_B_refined2.6646.8991685
X-RAY DIFFRACTIONr_long_range_B_other2.4676.3561560
X-RAY DIFFRACTIONr_rigid_bond_restr12.18632788
X-RAY DIFFRACTIONr_sphericity_free14.112528
X-RAY DIFFRACTIONr_sphericity_bonded6.31952942
LS refinement shellResolution: 0.869→0.891 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 364 -
Rwork0.174 7244 -
obs--97.48 %

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