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- PDB-7fw4: Crystal Structure of human FABP4 soaked with glycerol -

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Basic information

Entry
Database: PDB / ID: 7fw4
TitleCrystal Structure of human FABP4 soaked with glycerol
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 protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / 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)15,3985
Polymers15,0221
Non-polymers3764
Water2,216123
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)35.276, 54.706, 74.603
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.66 %
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: 0.99998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.44→44.12 Å / Num. obs: 26731 / % possible obs: 99.4 % / Redundancy: 6.06 % / Biso Wilson estimate: 29.559 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Rsym value: 0.045 / Χ2: 0.862 / Net I/σ(I): 15.98 / Num. measured all: 161705 / Scaling rejects: 152
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
1.44-1.485.7311.3541.1911056195919290.6471.49298.5
1.48-1.525.8081.1081.4910785188718570.7481.21898.4
1.52-1.565.550.7962.0810151184718290.8520.8899
1.56-1.615.9160.5163.2210602181117920.9260.56799
1.61-1.666.3050.4213.910940174517350.9580.45999.4
1.66-1.726.2690.2795.7210557169516840.980.30599.4
1.72-1.796.1320.2336.739958163416240.9870.25599.4
1.79-1.865.7710.1649.299118159115800.9920.1899.3
1.86-1.946.3120.114.269481151515020.9970.10999.1
1.94-2.046.4340.07518.489239144814360.9980.08299.2
2.04-2.156.410.06123.168839138513790.9990.06699.6
2.15-2.286.1720.05327.218060131613060.9980.05799.2
2.28-2.435.790.04730.067180124712400.9990.05199.4
2.43-2.636.5630.0437.167580115811550.9990.04399.7
2.63-2.886.390.03541.426939108710860.9990.03999.9
2.88-3.226.0370.03645.5158869859750.9990.03999
3.22-3.725.8030.0348.6650148688640.9990.03399.5
3.72-4.556.3680.0354.0647707507490.9990.03299.9
4.55-6.445.7370.0351.9434486026010.9980.03399.8
6.44-44.115.6960.02950.8821023713690.9990.03199.5

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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: 1.44→44.11 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.001 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 30 vol-% glycerol (3.26M) soaked into crystal, two molecules bind at surface but none at ligand binding site. test performed upon request based on hypothesis that glycerol in protein ...Details: 30 vol-% glycerol (3.26M) soaked into crystal, two molecules bind at surface but none at ligand binding site. test performed upon request based on hypothesis that glycerol in protein preparation might influence binding and/or in vivo results. No binding of glycerol at ligand binding site.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1284 5.2 %RANDOM
Rwork0.1994 ---
obs0.2008 23574 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.81 Å2 / Biso mean: 25.57 Å2 / Biso min: 13.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--0.18 Å20 Å2
3----2.1 Å2
Refinement stepCycle: final / Resolution: 1.44→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 22 123 1195
Biso mean--43.31 34.84 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021185
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9741616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6142552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67615238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.127157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02865
LS refinement shellResolution: 1.44→1.477 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 91 -
Rwork0.406 1512 -
all-1603 -
obs--81.91 %

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