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- PDB-7ego: X-ray structure of the human heart fatty acid-binding protein com... -

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Basic information

Entry
Database: PDB / ID: 7ego
TitleX-ray structure of the human heart fatty acid-binding protein complexed with the fluorescent probe HA527
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP / Complex / Binding protein / fluorescent probe
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
Chem-J3R / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsTakabayashi, M. / Yokota, J. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Sugiyama, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
Japan Science and TechnologyJPMJTM19DC Japan
Other private09-003-005 Japan
CitationJournal: To Be Published
Title: X-ray structure of the human heart fatty acid-binding protein complexed with the fluorescent probe HA527
Authors: Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Sugiyama, S.
History
DepositionMar 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 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)15,7104
Polymers14,8791
Non-polymers8313
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-3 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.521, 69.657, 33.844
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-J3R / 3-[methyl-(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]propanoic acid


Mass: 266.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / 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.: 154 / 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: 43.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / 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: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→42.93 Å / Num. obs: 40169 / % possible obs: 94.5 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.77
Reflection shellResolution: 1.21→1.28 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 4825

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WVM

3wvm


Resolution: 1.21→42.93 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.821 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15159 1977 5.2 %RANDOM
Rwork0.12913 ---
obs0.13034 36314 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.07 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.21→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 45 154 1235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0131246
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171208
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.6951690
X-RAY DIFFRACTIONr_angle_other_deg1.6581.6482825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.05523.65452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25715238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.929155
X-RAY DIFFRACTIONr_chiral_restr0.2150.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021390
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02242
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_it1.3870.956604
X-RAY DIFFRACTIONr_mcbond_other1.3720.954603
X-RAY DIFFRACTIONr_mcangle_it1.4411.442776
X-RAY DIFFRACTIONr_mcangle_other1.4441.444777
X-RAY DIFFRACTIONr_scbond_it2.6341.313642
X-RAY DIFFRACTIONr_scbond_other2.6351.313642
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6861.84915
X-RAY DIFFRACTIONr_long_range_B_refined2.75412.9951388
X-RAY DIFFRACTIONr_long_range_B_other2.58512.4451354
X-RAY DIFFRACTIONr_rigid_bond_restr5.28632452
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.21→1.24 Å
RfactorNum. reflection% reflection
Rfree0.137 100 -
Rwork-1733 -
obs--63.73 %

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