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- PDB-7fz9: Crystal Structure of human FABP4 in complex with N-methyl-6-(3-me... -

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Basic information

Entry
Database: PDB / ID: 7fz9
TitleCrystal Structure of human FABP4 in complex with N-methyl-6-(3-methylthiophen-2-yl)-4-phenyl-N-propan-2-yl-3-(1H-tetrazol-5-yl)pyridin-2-amine
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-WER / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Kuhne, 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 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)15,5874
Polymers15,0221
Non-polymers5653
Water4,324240
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)32.295, 53.986, 75.240
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-WER / (3M,6P)-N-methyl-6-(3-methylthiophen-2-yl)-4-phenyl-N-(propan-2-yl)-3-(1H-tetrazol-5-yl)pyridin-2-amine


Mass: 390.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22N6S / 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: 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.: 240 / 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: 43.66 %
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: Dec 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70003 Å / Relative weight: 1
ReflectionResolution: 0.96→37.62 Å / Num. obs: 81182 / % possible obs: 100 % / Redundancy: 6.46 % / Biso Wilson estimate: 12.693 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.036 / Rsym value: 0.034 / Χ2: 0.877 / Net I/σ(I): 18.76 / Num. measured all: 526267 / Scaling rejects: 36
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
0.96-0.986.3361.31.3437760596759600.5451.41799.9
0.98-1.016.1370.981.7835464578257790.6641.07199.9
1.01-1.046.7230.6532.7937734562156130.8520.70899.9
1.04-1.076.6890.4454.0536463545354510.9230.483100
1.07-1.116.5930.3115.6634965530553030.960.338100
1.11-1.156.420.237.5432900513151250.9760.2599.9
1.15-1.196.1930.1869.1430675495849530.9820.20399.9
1.19-1.246.790.15611.332641481048070.990.16999.9
1.24-1.296.7420.1313.230776456945650.9920.14199.9
1.29-1.366.6850.10316.4129422440344010.9950.112100
1.36-1.436.4440.08619.5326889417341730.9960.094100
1.43-1.526.2060.06524.8624613396639660.9970.071100
1.52-1.626.8350.04734.7525625375137490.9990.05199.9
1.62-1.756.740.03742.3323576349834980.9990.04100
1.75-1.926.5140.02953.3421085323832370.9990.032100
1.92-2.155.8270.02264.45170922934293310.025100
2.15-2.486.5860.0275.86172282617261610.022100
2.48-3.046.510.01883.87144522222222010.01999.9
3.04-4.295.8190.01589.84102351763175910.01699.8
4.29-37.616.3180.01394.4666721059105610.01499.7

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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: 0.96→37.61 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.574 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: two conformations, oe of them has significant distortion but is supported by electron density
RfactorNum. reflection% reflectionSelection details
Rfree0.1536 3976 5 %RANDOM
Rwork0.1339 ---
obs0.1349 74833 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: 59.34 Å2 / Biso mean: 13.314 Å2 / Biso min: 5.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 0.96→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 107 240 1387
Biso mean--15.2 24.09 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021201
X-RAY DIFFRACTIONr_bond_other_d0.0020.021201
X-RAY DIFFRACTIONr_angle_refined_deg2.5062.0191636
X-RAY DIFFRACTIONr_angle_other_deg0.9713.0012739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13224.69449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05715232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.275157
X-RAY DIFFRACTIONr_chiral_restr0.1720.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
X-RAY DIFFRACTIONr_rigid_bond_restr7.132402
X-RAY DIFFRACTIONr_sphericity_free22.492542
X-RAY DIFFRACTIONr_sphericity_bonded10.17852564
LS refinement shellResolution: 0.96→0.985 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 267 -
Rwork0.33 4823 -
all-5090 -
obs--89.24 %

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