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- PDB-7yf1: Structure of FABP at 1.7 Angstroms resolution. -

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Basic information

Entry
Database: PDB / ID: 7yf1
TitleStructure of FABP at 1.7 Angstroms resolution.
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP
Function / homology
Function and homology information


icosatetraenoic acid binding / Triglyceride catabolism / 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 transmembrane transporter activity ...icosatetraenoic acid binding / Triglyceride catabolism / 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 transmembrane transporter activity / long-chain fatty acid binding / sarcoplasm / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / fatty acid binding / extracellular space / nucleus / cytoplasm / 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
Similarity search - Domain/homology
PALMITIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, Y.h. / Wang, L.l.
Funding support China, 2items
OrganizationGrant numberCountry
Other governmentChina Postdoctoral Science Foundation:2020M682420 China
Other governmentGuangzhou International Collaborative Grant:2019A050510027 China
CitationJournal: Life / Year: 2022
Title: Structural Insights into Mouse H-FABP.
Authors: Wang, L. / Zhang, H. / Lv, P. / Li, Y. / Teng, M. / Liu, Y. / Wu, D.
History
DepositionJul 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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)16,0672
Polymers15,8111
Non-polymers2561
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint1 kcal/mol
Surface area7060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.305, 54.419, 65.387
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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


Mass: 15810.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fabp3, Fabph1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P11404
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 25% PEG 2000 MME, 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.7→41.83 Å / Num. obs: 15182 / % possible obs: 99.82 % / Redundancy: 1.1 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 1 / Net I/σ(I): 27.2
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 1456 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DENZOdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G5W

1g5w


Resolution: 1.7→41.83 Å / SU ML: 0.193 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.3159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 760 5.01 %
Rwork0.1685 14422 -
obs0.1698 15182 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 18 212 1268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561076
X-RAY DIFFRACTIONf_angle_d0.85511449
X-RAY DIFFRACTIONf_chiral_restr0.0587173
X-RAY DIFFRACTIONf_plane_restr0.0061180
X-RAY DIFFRACTIONf_dihedral_angle_d9.3495154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.22581670.21092786X-RAY DIFFRACTION99.09
1.83-2.020.19241380.1642847X-RAY DIFFRACTION100
2.02-2.310.19871380.17252874X-RAY DIFFRACTION100
2.31-2.910.19641680.1812874X-RAY DIFFRACTION100
2.91-41.830.19051490.15423041X-RAY DIFFRACTION100

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