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- PDB-7fww: Crystal Structure of human FABP4 in complex with (3-bromophenyl)-... -

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Basic information

Entry
Database: PDB / ID: 7fww
TitleCrystal Structure of human FABP4 in complex with (3-bromophenyl)-[(2Z)-2-phenylimino-1,3-thiazepan-3-yl]methanone
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-Q6I / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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)15,6505
Polymers15,0221
Non-polymers6274
Water4,017223
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)32.504, 53.841, 75.144
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-Q6I / (3-bromophenyl)[(2Z)-2-(phenylimino)-1,3-thiazepan-3-yl]methanone


Mass: 389.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17BrN2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
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: 0.70003 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70003 Å / Relative weight: 1
ReflectionResolution: 1.05→37.57 Å / Num. obs: 62379 / % possible obs: 99.9 % / Redundancy: 6.55 % / Biso Wilson estimate: 14.082 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.056 / Rsym value: 0.051 / Χ2: 0.859 / Net I/σ(I): 14.55 / Num. measured all: 406491 / Scaling rejects: 4
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
1.05-1.086.661.1221.6730148453445270.6621.21799.8
1.08-1.116.6350.8042.3329253441244090.7880.87399.9
1.11-1.146.5510.6043.0428360433043290.8710.657100
1.14-1.176.4230.4853.7227007420642050.9070.528100
1.17-1.216.0720.424.2324702407540680.9250.4699.8
1.21-1.256.5220.3415.3125736394639460.9540.371100
1.25-1.36.7760.2766.5225823381138110.9710.299100
1.3-1.366.7330.2297.7424772367936790.9780.248100
1.36-1.426.6760.1899.4223520352335230.9830.205100
1.42-1.486.4830.14211.9721951338633860.9890.155100
1.48-1.576.1250.10714.7719722322232200.9940.11799.9
1.57-1.666.9180.0820.7621099305030500.9970.086100
1.66-1.776.8510.06425.6319691287428740.9980.069100
1.77-1.926.6810.04831.7618092270827080.9990.052100
1.92-2.16.3080.03838.6615663248324830.9990.042100
2.1-2.356.0940.03443.1313828227122690.9990.03799.9
2.35-2.716.6990.03148.9913465201020100.9990.034100
2.71-3.326.3860.02952.8110926171417110.9990.03199.8
3.32-4.75.6930.02654.497777136913660.9990.02999.8
4.7-37.586.1110.02756.3649568138110.9990.02999.8

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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: 1.05→37.58 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.865 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: bromine atom, although damaged by radiation, enough to SAD-phase structure using Shelxde
RfactorNum. reflection% reflectionSelection details
Rfree0.1644 3073 5.1 %RANDOM
Rwork0.1354 ---
obs0.1369 57296 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.99 Å2 / Biso mean: 15.485 Å2 / Biso min: 6.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.05→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 55 224 1325
Biso mean--19.2 27.71 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021198
X-RAY DIFFRACTIONr_bond_other_d0.0030.021201
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.9881633
X-RAY DIFFRACTIONr_angle_other_deg1.0573.0022752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71225.47253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1315240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8156
X-RAY DIFFRACTIONr_chiral_restr0.1540.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
X-RAY DIFFRACTIONr_rigid_bond_restr5.06332399
X-RAY DIFFRACTIONr_sphericity_free25.02553
X-RAY DIFFRACTIONr_sphericity_bonded11.56552535
LS refinement shellResolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 190 -
Rwork0.282 3922 -
all-4112 -
obs--90.85 %

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