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Yorodumi- PDB-1gwx: MOLECULAR RECOGNITION OF FATTY ACIDS BY PEROXISOME PROLIFERATOR-A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gwx | ||||||
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Title | MOLECULAR RECOGNITION OF FATTY ACIDS BY PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS | ||||||
Components | PROTEIN (PPAR-DELTA) | ||||||
Keywords | TRANSCRIPTION / PPAR / FATTY ACIDS / NUCLEAR RECEPTOR FOLD | ||||||
Function / homology | Function and homology information fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / Carnitine metabolism / negative regulation of myoblast differentiation / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fatty acid metabolic process / cell-substrate adhesion / fatty acid beta-oxidation / negative regulation of cholesterol storage / decidualization / keratinocyte proliferation / fatty acid transport / positive regulation of fat cell differentiation / cellular response to nutrient levels / adipose tissue development / energy homeostasis / embryo implantation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / hormone-mediated signaling pathway / cholesterol metabolic process / negative regulation of miRNA transcription / fatty acid metabolic process / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / glucose metabolic process / negative regulation of epithelial cell proliferation / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / lipid binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Xu, H.E. / Lambert, M.H. / Montana, V.G. / Park, D.J. / Blanchard, S. / Brown, P. / Sternbach, D. / Lehmann, J. / Bruce, G.W. / Willson, T.M. ...Xu, H.E. / Lambert, M.H. / Montana, V.G. / Park, D.J. / Blanchard, S. / Brown, P. / Sternbach, D. / Lehmann, J. / Bruce, G.W. / Willson, T.M. / Kliewer, S.A. / Milburn, M.V. | ||||||
Citation | Journal: Mol.Cell / Year: 1999 Title: Molecular recognition of fatty acids by peroxisome proliferator-activated receptors. Authors: Xu, H.E. / Lambert, M.H. / Montana, V.G. / Parks, D.J. / Blanchard, S.G. / Brown, P.J. / Sternbach, D.D. / Lehmann, J.M. / Wisely, G.B. / Willson, T.M. / Kliewer, S.A. / Milburn, M.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gwx.cif.gz | 122.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gwx.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/1gwx ftp://data.pdbj.org/pub/pdb/validation_reports/gw/1gwx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31017.061 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD / Plasmid: PSETA WITH T7 PROMOTER / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE30) / References: UniProt: Q03181 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.98 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. obs: 40000 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. obs: 22731 / % possible obs: 94.5 % / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 1262531.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 94.38 Å2 / ksol: 0.533 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10.2 % / Rfactor obs: 0.238 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.326 / % reflection Rfree: 11.4 % / Rfactor Rwork: 0.281 |