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- PDB-7fwo: Crystal Structure of human FABP4 in complex with 2-cyclohexyl-6-h... -

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Basic information

Entry
Database: PDB / ID: 7fwo
TitleCrystal Structure of human FABP4 in complex with 2-cyclohexyl-6-hydroxy-1-benzofuran-3-one
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-OM6 / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Boehringer, M. / 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)15,4935
Polymers15,0221
Non-polymers4704
Water3,675204
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)32.504, 53.931, 74.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-OM6 / (2S)-2-cyclohexyl-6-hydroxy-1-benzofuran-3(2H)-one


Mass: 232.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 204 / 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: 43.7 %
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: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→37.45 Å / Num. obs: 50793 / % possible obs: 99.2 % / Redundancy: 6.11 % / Biso Wilson estimate: 13.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.035 / Rsym value: 0.037 / Χ2: 0.976 / Net I/σ(I): 24.62 / Num. measured all: 307917
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
1.12-1.154.6050.1539.6215400371033440.9810.17390.1
1.15-1.185.9970.13712.7321698362236180.990.15199.9
1.18-1.225.9730.12613.6321144354935400.9910.13899.7
1.22-1.255.910.11115.3120554348034780.9930.12299.9
1.25-1.36.4020.09417.7121236331833170.9960.103100
1.3-1.346.3680.08419.6520665324632450.9960.092100
1.34-1.396.2050.07521.5919193309530930.9960.08299.9
1.39-1.456.070.06624.0918179300029950.9970.07399.8
1.45-1.516.5410.05827.819016290929070.9980.06499.9
1.51-1.596.5060.04833.117918275527540.9980.053100
1.59-1.676.3870.04436.0316914265126480.9990.04799.9
1.67-1.775.9320.03938.9114860251225050.9980.04399.7
1.77-1.96.6010.03445.9215539235723540.9990.03799.9
1.9-2.056.3970.0350.5914156222022130.9990.03399.7
2.05-2.246.1290.02852.6912387203020210.9990.03199.6
2.24-2.515.5030.02751.6110246187618620.9990.0399.3
2.51-2.96.3130.02657.8110341164116380.9990.02999.8
2.9-3.556.020.02658.718573143014240.9990.02899.6
3.55-5.025.4330.02557.265976111411000.9990.02898.7
5.02-37.455.8360.02858.4739226806720.9980.03198.8

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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: 1.12→37.45 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.655 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1585 2544 5 %RANDOM
Rwork0.131 ---
obs0.1324 47948 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 53.61 Å2 / Biso mean: 11.547 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.42 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.12→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 30 204 1274
Biso mean--16.85 22.36 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021173
X-RAY DIFFRACTIONr_bond_other_d0.0040.02807
X-RAY DIFFRACTIONr_angle_refined_deg2.1641.981591
X-RAY DIFFRACTIONr_angle_other_deg1.3631995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.61325.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79815234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.098156
X-RAY DIFFRACTIONr_chiral_restr0.1250.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021295
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02227
X-RAY DIFFRACTIONr_rigid_bond_restr5.57331980
X-RAY DIFFRACTIONr_sphericity_free14.714537
X-RAY DIFFRACTIONr_sphericity_bonded7.71552123
LS refinement shellResolution: 1.122→1.152 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.151 136 -
Rwork0.107 2953 -
all-3089 -
obs--87.73 %

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