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- PDB-7g10: Crystal Structure of human FABP4 binding site mutated to that of ... -

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Basic information

Entry
Database: PDB / ID: 7g10
TitleCrystal Structure of human FABP4 binding site mutated to that of FABP3 in complex with 1-[(4-chloro-2-phenoxyphenyl)methyl]-4-hydroxypyridin-2-one
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-WMF / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Obst-Sander, 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 binding site mutated to that of FABP3 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)15,6245
Polymers15,0601
Non-polymers5644
Water2,612145
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)32.532, 53.972, 74.911
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: 15060.242 Da / Num. of mol.: 1 / Mutation: V23L,M40T,I51L,S53T,I104L,V115L,C117L,S124C
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-WMF / 4-hydroxy-1-[(2-phenoxyphenyl)methyl]pyridin-2(1H)-one


Mass: 293.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 43.67 %
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: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.26→37.46 Å / Num. obs: 35798 / % possible obs: 98.1 % / Redundancy: 5.714 % / Biso Wilson estimate: 20.369 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.078 / Χ2: 0.827 / Net I/σ(I): 12.15 / Num. measured all: 204563 / Scaling rejects: 38
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
1.26-1.294.9011.4521.1811949265624380.5091.61991.8
1.29-1.334.9951.2461.3712022257024070.5861.38793.7
1.33-1.375.0151.1451.5612047253024020.6321.27494.9
1.37-1.414.9271.0741.7111750245223850.6511.19997.3
1.41-1.455.2210.8322.2712082234923140.7640.92498.5
1.45-1.515.6690.6133.0613140233023180.870.67599.5
1.51-1.565.9240.454.3213057221322040.9380.49399.6
1.56-1.636.0490.3765.4413041215921560.9470.41299.9
1.63-1.76.0470.2926.9412361204720440.9650.3299.9
1.7-1.785.8480.2248.8311503197119670.9810.24699.8
1.78-1.886.5730.14912.5712397188818860.9940.16299.9
1.88-1.996.5240.09617.6911625178517820.9960.10499.8
1.99-2.136.4030.07921.2310738167816770.9970.08699.9
2.13-2.36.1270.06624.719625157615710.9970.07299.7
2.3-2.525.5550.05626.198072146814530.9980.06299
2.52-2.826.5320.04533.268589131813150.9990.04999.8
2.82-3.256.250.03938.667456119511930.9980.04299.8
3.25-3.985.8950.03143.015901100910010.9990.03499.2
3.98-5.635.5080.02942.5243848067960.9990.03298.8
5.63-37.465.7750.02843.828244934890.9990.0399.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0403refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.26→37.46 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.404 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: only spurious density for chlorine atom was probably radiolyzed by X-rays rest of ligand very well defined use coordinates with caution - ligand may have shifted after radiolysis
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 1711 5.1 %RANDOM
Rwork0.164 ---
obs0.1664 31841 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.73 Å2 / Biso mean: 15.903 Å2 / Biso min: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å20 Å2
2---1.16 Å20 Å2
3----1.75 Å2
Refinement stepCycle: final / Resolution: 1.26→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 36 145 1231
Biso mean--20.08 29.26 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0121119
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161074
X-RAY DIFFRACTIONr_angle_refined_deg2.1271.6741511
X-RAY DIFFRACTIONr_angle_other_deg0.831.5952480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.88356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21710211
X-RAY DIFFRACTIONr_chiral_restr0.1160.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
X-RAY DIFFRACTIONr_mcbond_it1.31.424541
X-RAY DIFFRACTIONr_mcbond_other1.2951.423541
X-RAY DIFFRACTIONr_mcangle_it1.5882.56676
X-RAY DIFFRACTIONr_rigid_bond_restr5.93632193
LS refinement shellResolution: 1.26→1.293 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 107 -
Rwork0.364 1980 -
all-2087 -
obs--78.75 %

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