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- PDB-7fwc: Crystal Structure of human FABP4 in complex with 5-(4-chloropheny... -

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Basic information

Entry
Database: PDB / ID: 7fwc
TitleCrystal Structure of human FABP4 in complex with 5-(4-chlorophenyl)-2-(hydroxymethylene)cyclohexane-1,3-dione
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
Chem-M69 / 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)15,3693
Polymers15,0221
Non-polymers3472
Water2,702150
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)32.354, 54.036, 75.087
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-M69 / (2seqTrans,5S)-5-(4-chlorophenyl)-2-(hydroxymethylidene)cyclohexane-1,3-dione


Mass: 250.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11ClO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 43.7 %
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: 1.00002 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.12→37.54 Å / Num. obs: 50959 / % possible obs: 99.2 % / Redundancy: 5.98 % / Biso Wilson estimate: 16.685 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.039 / Rsym value: 0.038 / Χ2: 0.91 / Net I/σ(I): 17.02 / Num. measured all: 303749 / Scaling rejects: 5
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
1.12-1.154.2610.5012.7614158376333230.8260.56788.3
1.15-1.185.8480.4324.1321251363736340.9140.47599.9
1.18-1.225.7760.4044.5820405354535330.9270.44599.7
1.22-1.255.7180.3255.4419904348934810.9570.35899.8
1.25-1.296.2210.257.0220885336333570.9740.27399.8
1.29-1.346.2070.2048.6320097324132380.980.22399.9
1.34-1.396.0280.1769.9518754311531110.9840.19399.9
1.39-1.456.0020.13312.8318235303830380.990.146100
1.45-1.516.4240.10116.6118661290629050.9930.111100
1.51-1.586.3980.07721.5217773277927780.9970.084100
1.58-1.676.2410.06325.6116564265726540.9970.06999.9
1.67-1.775.8380.05329.5614654251325100.9980.05899.9
1.77-1.896.4860.04137.9915463238623840.9990.04599.9
1.89-2.056.3580.03643.9414147222822250.9990.03999.9
2.05-2.246.0970.03346.7512365203520280.9990.03699.7
2.24-2.515.4870.03246.2910332188718830.9990.03599.8
2.51-2.896.4540.02953.5410682165616550.9990.03299.9
2.89-3.546.270.02555.118909142414210.9990.02899.8
3.54-5.015.6130.02353.556298112811220.9990.02599.5
5.01-37.566.2220.02155.3842126846770.9990.02399

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Processing

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

Resolution: 1.12→37.56 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.921 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: hydroxy derivative identified by electron density and confirmed by MS. two conformations of ligand with different pseudo-chirality at C4
RfactorNum. reflection% reflectionSelection details
Rfree0.1618 2516 5 %RANDOM
Rwork0.1362 ---
obs0.1375 47338 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.61 Å2 / Biso mean: 17.314 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---0.24 Å20 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 1.12→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 61 150 1251
Biso mean--19.45 26.87 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021202
X-RAY DIFFRACTIONr_bond_other_d0.0020.021216
X-RAY DIFFRACTIONr_angle_refined_deg2.2071.9981640
X-RAY DIFFRACTIONr_angle_other_deg0.8583.0012783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52325.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81415241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.673156
X-RAY DIFFRACTIONr_chiral_restr0.1260.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
X-RAY DIFFRACTIONr_rigid_bond_restr5.70432418
X-RAY DIFFRACTIONr_sphericity_free23.59538
X-RAY DIFFRACTIONr_sphericity_bonded12.63352499
LS refinement shellResolution: 1.121→1.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 156 -
Rwork0.244 2749 -
all-2905 -
obs--81.28 %

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