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- PDB-7fyb: Crystal Structure of human FABP4 in complex with rac-(1R,2S,4R)-2... -

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Basic information

Entry
Database: PDB / ID: 7fyb
TitleCrystal Structure of human FABP4 in complex with rac-(1R,2S,4R)-2-[(3-chlorobenzoyl)amino]-4-phenoxycyclohexane-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-VIY / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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)15,7126
Polymers15,0221
Non-polymers6905
Water2,648147
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)32.564, 53.666, 74.652
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, 152 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-VIY / (1R,2S,4R)-2-(3-chlorobenzamido)-4-phenoxycyclohexane-1-carboxylic acid


Mass: 373.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20ClNO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
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: 0.7 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.08→43.57 Å / Num. obs: 56955 / % possible obs: 99.9 % / Redundancy: 6.57 % / Biso Wilson estimate: 15.108 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.052 / Rsym value: 0.046 / Χ2: 0.853 / Net I/σ(I): 15.34 / Num. measured all: 404085 / Scaling rejects: 29
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
1.05-1.086.4561.4751.1228949449144840.481.60599.8
1.08-1.116.0981.0171.6126855441444040.661.11399.8
1.11-1.146.6830.7892.2528685429542920.7850.85599.9
1.14-1.176.7370.6062.9328053416741640.8640.65799.9
1.17-1.216.620.4993.5126760404540420.9090.54299.9
1.21-1.256.520.4174.2225570392639220.9290.45399.9
1.25-1.36.1680.337523148376237530.9470.36899.8
1.3-1.366.640.2736.3924329366836640.9680.29799.9
1.36-1.426.8090.2267.9423826350134990.9750.24599.9
1.42-1.486.7950.16910.3722728334733450.9850.18399.9
1.48-1.576.6850.12812.9821318319331890.9920.13999.9
1.57-1.666.2180.09217.0818873303630350.9940.101100
1.66-1.776.7830.07322.0519304284728460.9970.079100
1.77-1.926.8740.05330.0718421268026800.9980.057100
1.92-2.16.740.03939.3616506245024490.9990.042100
2.1-2.356.1540.03444.0313883225822560.9990.03799.9
2.35-2.716.4580.0351.112916200120000.9990.033100
2.71-3.326.5650.02559.22111811703170310.027100
3.32-4.75.8530.0265.697925136013540.9990.02299.6
4.7-43.576.0390.01966.19485580780410.02199.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0018refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.05→43.57 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.995 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ligand has two conformations at 3-Chloro-benzoylamino part a second conformation of the carboxylate is present but not different enough to warrant building (i.e. the carboxylate is somewhat flexible)
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 3075 5.2 %RANDOM
Rwork0.1498 ---
obs0.1514 56561 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.47 Å2 / Biso mean: 16.85 Å2 / Biso min: 7.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.05→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 107 148 1305
Biso mean--17.17 27.84 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021189
X-RAY DIFFRACTIONr_bond_other_d0.0020.021171
X-RAY DIFFRACTIONr_angle_refined_deg2.4272.0151611
X-RAY DIFFRACTIONr_angle_other_deg1.6433.0012675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1532548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.604156
X-RAY DIFFRACTIONr_chiral_restr0.1370.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02257
X-RAY DIFFRACTIONr_rigid_bond_restr6.79332360
X-RAY DIFFRACTIONr_sphericity_free23.232553
X-RAY DIFFRACTIONr_sphericity_bonded13.27952431
LS refinement shellResolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 212 -
Rwork0.351 3764 -
all-3976 -
obs--88.67 %

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