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- PDB-7fwn: Crystal Structure of human FABP4 in complex with 3-(5-methyl-2,3-... -

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Basic information

Entry
Database: PDB / ID: 7fwn
TitleCrystal Structure of human FABP4 in complex with 3-(5-methyl-2,3-diphenylindol-1-yl)propanoic 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
Chem-OKF / 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. / 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)15,5704
Polymers15,0221
Non-polymers5483
Water3,567198
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)32.254, 53.714, 75.386
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OKF / 3-(5-methyl-2,3-diphenyl-1H-indol-1-yl)propanoic acid


Mass: 355.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
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: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.12→37.69 Å / Num. obs: 50163 / % possible obs: 98.3 % / Redundancy: 5.569 % / Biso Wilson estimate: 13.937 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.066 / Χ2: 0.949 / Net I/σ(I): 15.84 / Num. measured all: 279342
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
1.12-1.154.3650.2974.6813528373430990.9340.33583
1.15-1.185.3980.2536.3319315360535780.9570.28199.3
1.18-1.225.3590.227.1118763352335010.9650.24599.4
1.22-1.255.3020.1917.9218213344534350.9760.21399.7
1.25-1.35.7890.1559.4419011330732840.9850.17199.3
1.3-1.345.7530.13510.5318587324332310.9890.14999.6
1.34-1.395.630.11911.9417363310230840.9880.13299.4
1.39-1.455.5280.10713.2816336297329550.9890.11899.4
1.45-1.515.9850.09315.9117196288528730.9930.10299.6
1.51-1.595.9010.08118.4116257276627550.9940.08999.6
1.59-1.675.7890.0742015208263426270.9940.08299.7
1.67-1.775.3850.06721.4113377249524840.9950.07499.6
1.77-1.95.9390.05924.4714010236323590.9960.06599.8
1.9-2.055.8940.05626.612913220121910.9960.06199.5
2.05-2.245.760.05527.1611583201620110.9960.0699.8
2.24-2.515.2120.05326.589730187218670.9960.05999.7
2.51-2.96.1050.05129.739970163516330.9970.05699.9
2.9-3.555.860.05129.768275141814120.9970.05699.6
3.55-5.025.2420.0528.495798111311060.9960.05699.4
5.02-37.695.7650.04529.3739096816780.9970.04999.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0093refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.12→37.69 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.793 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1526 2485 5 %RANDOM
Rwork0.1342 ---
obs0.1351 47065 97.26 %-
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: 43.08 Å2 / Biso mean: 10.882 Å2 / Biso min: 6.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2---0.24 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 1.12→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 37 202 1285
Biso mean--12.39 23.76 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221134
X-RAY DIFFRACTIONr_bond_other_d0.0020.02764
X-RAY DIFFRACTIONr_angle_refined_deg1.9341.9911538
X-RAY DIFFRACTIONr_angle_other_deg0.9431877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5385145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05324.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90215216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.085156
X-RAY DIFFRACTIONr_chiral_restr0.110.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02227
X-RAY DIFFRACTIONr_rigid_bond_restr4.34336392
X-RAY DIFFRACTIONr_sphericity_free15.1315205
X-RAY DIFFRACTIONr_sphericity_bonded5.85351877
LS refinement shellResolution: 1.122→1.151 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 134 -
Rwork0.178 2659 -
all-2793 -
obs--77.99 %

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