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- PDB-7g0i: Crystal Structure of human FABP4 in complex with 5-phenoxy-6-(2,2... -

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Basic information

Entry
Database: PDB / ID: 7g0i
TitleCrystal Structure of human FABP4 in complex with 5-phenoxy-6-(2,2,2-trifluoroethoxy)-2-(trifluoromethyl)pyridine-3-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
Chem-TXO / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Richter, H. / 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

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, adipocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,14211
Polymers15,0221
Non-polymers1,12010
Water2,324129
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)32.446, 53.543, 74.681
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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-TXO / 5-phenoxy-6-(2,2,2-trifluoroethoxy)-2-(trifluoromethyl)pyridine-3-carboxylic acid


Mass: 381.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H9F6NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
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: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70001 Å / Relative weight: 1
ReflectionResolution: 1.07→43.51 Å / Num. obs: 58224 / % possible obs: 99.9 % / Redundancy: 6.54 % / Biso Wilson estimate: 15.968 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.042 / Rsym value: 0.037 / Χ2: 0.853 / Net I/σ(I): 18.28 / Num. measured all: 380024 / Scaling rejects: 24
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
1.07-1.16.4891.4251.2627533424542430.561.55100
1.1-1.136.18411.825390411241060.6941.09299.9
1.13-1.166.4690.7822.3526362408240750.7830.85199.8
1.16-1.26.7640.6173.0526432391339080.8740.66899.9
1.2-1.246.6980.5183.625313378437790.9030.56299.9
1.24-1.286.5640.4174.3924222369336900.9360.45399.9
1.28-1.336.3040.3225.4622215352835240.9570.35199.9
1.33-1.386.3470.2536.8721822343834380.9710.276100
1.38-1.446.8470.2028.9322589329932990.9810.219100
1.44-1.516.7790.15311.521319314631450.990.166100
1.51-1.66.6950.10616.1120226302230210.9950.115100
1.6-1.696.3150.08220.2317986284928480.9960.089100
1.69-1.816.5580.0627.2417654269226920.9980.065100
1.81-1.956.8950.04238.8917265250625040.9990.04599.9
1.95-2.146.740.03151.2415730233423340.9990.034100
2.14-2.396.350.02657.9913329210420990.9990.02999.8
2.39-2.766.2870.02366.88117631873187110.02599.9
2.76-3.386.6070.01883.31106701616161510.01999.9
3.38-4.795.9580.01494.1176201283127910.01599.7
4.79-43.5260.01393.75458476676410.01499.7

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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: 1.07→43.52 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.09 / SU ML: 0.023 / 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
Rfree0.1813 2894 5.2 %RANDOM
Rwork0.1515 ---
obs0.1531 53216 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: 69.14 Å2 / Biso mean: 17.302 Å2 / Biso min: 6.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 1.07→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 134 129 1313
Biso mean--25.46 27.76 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191178
X-RAY DIFFRACTIONr_bond_other_d0.0050.021185
X-RAY DIFFRACTIONr_angle_refined_deg2.2692.0031592
X-RAY DIFFRACTIONr_angle_other_deg1.0073.0032685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.54424.34846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72215217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.856157
X-RAY DIFFRACTIONr_chiral_restr0.160.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02249
X-RAY DIFFRACTIONr_rigid_bond_restr6.10232363
X-RAY DIFFRACTIONr_sphericity_free25.565538
X-RAY DIFFRACTIONr_sphericity_bonded12.94652439
LS refinement shellResolution: 1.07→1.098 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 187 -
Rwork0.361 3609 -
all-3796 -
obs--89.49 %

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