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Yorodumi- PDB-2zk2: Human peroxisome proliferator-activated receptor gamma ligand bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zk2 | ||||||
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Title | Human peroxisome proliferator-activated receptor gamma ligand binding domain complexed with glutathion conjugated 15-deoxy-delta12,14-prostaglandin J2 | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | TRANSCRIPTION / anti parallel helix sandwich / Activator / Alternative splicing / Diabetes mellitus / Disease mutation / DNA-binding / Metal-binding / Nucleus / Obesity / Phosphoprotein / Polymorphism / Receptor / Transcription regulation / Zinc / Zinc-finger | ||||||
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: 2.26 Å | ||||||
Authors | Waku, T. / Shiraki, T. / Oyama, T. / Fujimoto, Y. / Morikawa, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids Authors: Waku, T. / Shiraki, T. / Oyama, T. / Fujimoto, Y. / Maebara, K. / Kamiya, N. / Jingami, H. / Morikawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zk2.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zk2.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zk2_validation.pdf.gz | 963.2 KB | Display | wwPDB validaton report |
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Full document | 2zk2_full_validation.pdf.gz | 1013.3 KB | Display | |
Data in XML | 2zk2_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 2zk2_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/2zk2 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/2zk2 | HTTPS FTP |
-Related structure data
Related structure data | 2zk0C 2zk1C 2zk3C 2zk4C 2zk5C 1prgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32530.652 Da / Num. of mol.: 2 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: pparg / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P37231 #2: Chemical | ChemComp-GSH / | #3: Chemical | ChemComp-PTG / ( | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 0.8M Sodium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 11, 2007 |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 30883 / Num. obs: 30247 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.304 / Num. unique all: 2647 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PRG Resolution: 2.26→48.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 194687.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.0879 Å2 / ksol: 0.36226 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.26→48.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.39 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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