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- PDB-7fxr: Crystal Structure of human FABP4 in complex with 2-[rac-(9R,10S)-... -

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Basic information

Entry
Database: PDB / ID: 7fxr
TitleCrystal Structure of human FABP4 in complex with 2-[rac-(9R,10S)-10-benzyl-3,3-dimethyl-1,5-dioxaspiro[5.5]undecan-9-yl]acetic 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
FORMIC ACID / Chem-TQO / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Chen, J. / 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)15,5935
Polymers15,0221
Non-polymers5714
Water4,179232
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)32.424, 53.896, 74.808
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 / Fragment: SOLUBLE FORM, RESIDUES 3-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15090
#2: Chemical ChemComp-TQO / [(8R,9S)-8-benzyl-3,3-dimethyl-1,5-dioxaspiro[5.5]undecan-9-yl]acetic acid


Mass: 332.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O4 / 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.: 232 / 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: 43.46 %
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: 0.7 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.99→43.73 Å / Num. obs: 73866 / % possible obs: 100 % / Redundancy: 6.54 % / Biso Wilson estimate: 12.145 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.056 / Rsym value: 0.051 / Χ2: 0.858 / Net I/σ(I): 15.78 / Num. measured all: 487529 / Scaling rejects: 43
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
0.99-1.026.5451.251.3335522543254270.5771.35899.9
1.02-1.046.7090.8861.9434995521952160.7750.96199.9
1.04-1.076.7110.672.5934383512351230.8450.726100
1.07-1.116.6990.4593.7233165495349510.9150.498100
1.11-1.146.6410.3624.7532082483148310.9420.393100
1.14-1.186.4140.2955.6829921466646650.9590.321100
1.18-1.236.0810.2556.3827487452445200.9670.27999.9
1.23-1.286.9090.2197.9429984434043400.9810.237100
1.28-1.336.9090.1869.2328936418941880.9850.201100
1.33-1.46.8450.15611.1227346399539950.9870.169100
1.4-1.486.7630.12413.7325808381738160.9910.134100
1.48-1.576.5850.09616.823712360236010.9950.105100
1.57-1.676.0060.0721.4820378339333930.9970.077100
1.67-1.816.4650.05428.1520810322032190.9980.059100
1.81-1.986.9550.03839.4220246291229110.9990.041100
1.98-2.216.860.02949.7818315267026700.9990.031100
2.21-2.566.5990.02555.43158122397239610.027100
2.56-3.135.9230.02161.1120182030202910.023100
3.13-4.436.5490.02179.0610544161016100.9990.023100
4.43-43.736.3440.02678.1160659619560.9990.02999.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0119refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 0.99→43.73 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.686 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ligand numbering does not follow chemical name enantiomer is fixed by electron density as S-carboxylate, R-phenyl
RfactorNum. reflection% reflectionSelection details
Rfree0.1611 3554 5 %RANDOM
Rwork0.1377 ---
obs0.1389 67774 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.37 Å2 / Biso mean: 13.031 Å2 / Biso min: 5.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 0.99→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 64 235 1345
Biso mean--13.71 23.28 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021162
X-RAY DIFFRACTIONr_bond_other_d0.0010.021166
X-RAY DIFFRACTIONr_angle_refined_deg2.2091.9881579
X-RAY DIFFRACTIONr_angle_other_deg1.4633.0012668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92825.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94815228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.492156
X-RAY DIFFRACTIONr_chiral_restr0.1360.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
X-RAY DIFFRACTIONr_rigid_bond_restr5.08732328
X-RAY DIFFRACTIONr_sphericity_free16.091528
X-RAY DIFFRACTIONr_sphericity_bonded9.46552510
LS refinement shellResolution: 0.99→1.016 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 218 -
Rwork0.312 4417 -
all-4635 -
obs--89.48 %

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