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- PDB-7g1c: Crystal Structure of human FABP4 in complex with rac-(1R,2S)-2-[(... -

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Basic information

Entry
Database: PDB / ID: 7g1c
TitleCrystal Structure of human FABP4 in complex with rac-(1R,2S)-2-[(3-methylphenoxy)methyl]cyclohexane-1-carboxylic acid
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytosol / cytoplasm
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
FORMIC ACID / Chem-WNF / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Buettelmann, B. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human FABP4 complex
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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, adipocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4915
Polymers15,0221
Non-polymers4694
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.546, 53.825, 75.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fatty acid-binding protein, adipocyte / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP ...Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP / Fatty acid-binding protein 4


Mass: 15022.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090

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Non-polymers , 5 types, 230 molecules

#2: Chemical ChemComp-WNF / (1S,2R)-2-[(3-methylphenoxy)methyl]cyclohexane-1-carboxylic acid


Mass: 248.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.70001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70001 Å / Relative weight: 1
ReflectionResolution: 1.08→37.71 Å / Num. obs: 57651 / % possible obs: 99.9 % / Redundancy: 6.49 % / Biso Wilson estimate: 14.457 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.081 / Rsym value: 0.074 / Χ2: 0.818 / Net I/σ(I): 11.93 / Num. measured all: 372640 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.08-1.116.0341.4121.4125161418641700.5171.54599.6
1.11-1.146.6451.1031.9627160409140870.6541.19699.9
1.14-1.176.6270.8852.4726548401840060.7470.9699.7
1.17-1.216.5220.7512.8825377389338910.830.81699.9
1.21-1.256.4050.673.1923950374737390.8560.72999.8
1.25-1.296.0770.5433.7722120364636400.8890.59499.8
1.29-1.346.3790.4444.6822481352535240.9290.483100
1.34-1.396.7550.3755.7122898339033900.9430.406100
1.39-1.466.7160.2827.421906326232620.9620.306100
1.46-1.536.6820.2258.9420960313831370.9780.244100
1.53-1.616.3780.15212.1818982297929760.9880.16599.9
1.61-1.716.2580.11814.7217641282128190.9920.12899.9
1.71-1.836.8690.08719.8618252265826570.9960.094100
1.83-1.976.7290.06225.5616708248524830.9980.06799.9
1.97-2.166.5310.0531.0415165232323220.9980.054100
2.16-2.416.0170.04633.1812474207520730.9980.0599.9
2.41-2.796.6240.03839.0712288185618550.9990.04199.9
2.79-3.426.5920.03344.0510580160716050.9990.03699.9
3.42-4.835.8590.03146.577423126812670.9990.03599.9
4.83-37.726.0720.03246.7145667567520.9990.03599.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0119refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.08→37.72 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.177 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 2828 5.1 %RANDOM
Rwork0.1482 ---
obs0.15 52499 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.02 Å2 / Biso mean: 15.05 Å2 / Biso min: 5.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.76 Å20 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 1.08→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 49 232 1327
Biso mean--18.83 28.29 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021177
X-RAY DIFFRACTIONr_bond_other_d0.0020.021184
X-RAY DIFFRACTIONr_angle_refined_deg2.2951.9781596
X-RAY DIFFRACTIONr_angle_other_deg1.5463.0012717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2012552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14915238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.969157
X-RAY DIFFRACTIONr_chiral_restr0.1530.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_rigid_bond_restr6.69532361
X-RAY DIFFRACTIONr_sphericity_free28.266540
X-RAY DIFFRACTIONr_sphericity_bonded14.15452520
LS refinement shellResolution: 1.08→1.108 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 175 -
Rwork0.336 3353 -
all-3528 -
obs--88.31 %

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