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Yorodumi- PDB-4xld: Crystal structure of the human PPARg-LBD/rosiglitazone complex ob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xld | ||||||
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Title | Crystal structure of the human PPARg-LBD/rosiglitazone complex obtained by dry co-crystallization and in situ diffraction | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | GENE REGULATION / nuclear receptor ligand screening | ||||||
Function / homology | Function and homology information Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane ...Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane / aerobic respiration / mitochondrial inner membrane / mitochondrion / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Delfosse, V. / Guichou, J.-F. | ||||||
Funding support | France, 1items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Combining `dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography. Authors: Gelin, M. / Delfosse, V. / Allemand, F. / Hoh, F. / Sallaz-Damaz, Y. / Pirocchi, M. / Bourguet, W. / Ferrer, J.L. / Labesse, G. / Guichou, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xld.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xld.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xld_validation.pdf.gz | 725.3 KB | Display | wwPDB validaton report |
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Full document | 4xld_full_validation.pdf.gz | 727 KB | Display | |
Data in XML | 4xld_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 4xld_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/4xld ftp://data.pdbj.org/pub/pdb/validation_reports/xl/4xld | HTTPS FTP |
-Related structure data
Related structure data | 3rdcC 4xn6C 4xncC 4xneC 4xoyC 4xozC 4xp0C 4xp2C 4xp3C 4xrjC 4xrlC 4zscC 4zsdC 2prgS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 33752.066 Da / Num. of mol.: 1 / Fragment: UNP residues 203-477 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37231 |
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#2: Chemical | ChemComp-FMT / |
#3: Chemical | ChemComp-BRL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 3-4 M Sodium Formate / PH range: 7-7.5 |
-Data collection
Diffraction | Mean temperature: 291 K Ambient temp details: in situ (in plate), at room temperature |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97922 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→47.37 Å / Num. obs: 12488 / % possible obs: 90 % / Redundancy: 4.4 % / Biso Wilson estimate: 41.1 Å2 / Rsym value: 0.154 / Net I/σ(I): 7.43 |
Reflection shell | Resolution: 2.45→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 4.68 / % possible all: 77.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2prg Resolution: 2.45→47.369 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→47.369 Å
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Refine LS restraints |
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LS refinement shell |
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