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- PDB-7fxs: Crystal Structure of human FABP4 binding site mutated to that of ... -

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Basic information

Entry
Database: PDB / ID: 7fxs
TitleCrystal Structure of human FABP4 binding site mutated to that of FABP5 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: 1.25 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 binding site mutated to that of FABP5 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)15,6285
Polymers15,0121
Non-polymers6164
Water3,225179
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)32.141, 52.612, 72.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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: 15012.244 Da / Num. of mol.: 1 / Mutation: V24L,V33M,A34G,M41C,S54T,F58L,H94Q,S125C
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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.03 Å3/Da / Density % sol: 39.51 %
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: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→42.52 Å / Num. obs: 34854 / % possible obs: 100 % / Redundancy: 12.059 % / Biso Wilson estimate: 18.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.158 / Χ2: 0.859 / Net I/σ(I): 8.97 / Num. measured all: 420310 / Scaling rejects: 11
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
1.25-1.2810.4892.3970.7826736255025490.2632.518100
1.28-1.3212.2882.0021.130180245624560.4232.088100
1.32-1.3612.1661.7961.3229234240324030.4661.875100
1.36-1.411.4761.5771.5326956234923490.5121.651100
1.4-1.4412.7021.2522.128668225722570.6231.305100
1.44-1.4912.5971.12.5227524218521850.6861.147100
1.49-1.5512.1810.8593.526079214121410.8380.898100
1.55-1.6111.2390.6474.923028204920490.8890.68100
1.61-1.6912.3180.5056.3224143196219600.9440.52799.9
1.69-1.7712.5560.3748.523730189018900.9640.391100
1.77-1.8612.8980.27111.123178179717970.9860.282100
1.86-1.9812.3290.17914.2520971170117010.9940.186100
1.98-2.1112.150.14916.619658161816180.9930.156100
2.11-2.2813.0220.12219.7219481149614960.9960.127100
2.28-2.512.7030.10321.0817771139913990.9960.107100
2.5-2.811.7240.09821.9114831126612650.9960.10299.9
2.8-3.2311.6490.07924.2913187113211320.9970.083100
3.23-3.9511.890.06927.38114629649640.9970.072100
3.95-5.5910.730.0626.8583167757750.9980.063100
5.59-42.5211.0620.05626.5551774704680.9980.05999.6

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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: 1.25→42.52 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.799 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: merged data from two crystals
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1662 5 %RANDOM
Rwork0.1477 ---
obs0.1497 31349 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.13 Å2 / Biso mean: 14.358 Å2 / Biso min: 5.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.25→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 46 179 1237
Biso mean--16.23 26.45 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021100
X-RAY DIFFRACTIONr_bond_other_d0.0020.021098
X-RAY DIFFRACTIONr_angle_refined_deg2.19921490
X-RAY DIFFRACTIONr_angle_other_deg0.9283.0022502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33624.65143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3615216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.985157
X-RAY DIFFRACTIONr_chiral_restr0.1420.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_rigid_bond_restr5.24332193
X-RAY DIFFRACTIONr_sphericity_free25.874551
X-RAY DIFFRACTIONr_sphericity_bonded11.87252307
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 104 -
Rwork0.327 2043 -
all-2147 -
obs--85.06 %

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