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Yorodumi- PDB-1prg: LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1prg | ||||||
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Title | LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA | ||||||
Components | PROTEIN (PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA) | ||||||
Keywords | GENE REGULATION / THIAZOLIDINEDIONE / LIGAND-BINDING DOMAIN / NUCLEAR RECEPTOR / APO / TRANSCRIPTION FACTOR / ORPHAN RECEPTOR | ||||||
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 / MIR / Resolution: 2.2 Å | ||||||
Authors | Nolte, R.T. / Wisely, G.B. / Milburn, M.V. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma. Authors: Nolte, R.T. / Wisely, G.B. / Westin, S. / Cobb, J.E. / Lambert, M.H. / Kurokawa, R. / Rosenfeld, M.G. / Willson, T.M. / Glass, C.K. / 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 | 1prg.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1prg.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 1prg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1prg_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 1prg_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 1prg_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 1prg_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/1prg ftp://data.pdbj.org/pub/pdb/validation_reports/pr/1prg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.112745, 0.983997, 0.137977), |
-Components
#1: Protein | Mass: 30833.850 Da / Num. of mol.: 2 / Fragment: LBD (LIGAND BINDING DOMAIN), RESIDUES 207-476 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEAR / Gene: HUMAN PPAR GAMMA CDNA / Plasmid: PRSET A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): HPPARGAMMA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P37231 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: VAPOR DIFFUSION METHOD, HANGING DROP TECHNIQUE, 1.4M SODIUM CITRATE, 100MM HEPES, PH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→60 Å / Num. obs: 89611 / % possible obs: 85 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.264 / % possible all: 68 |
Reflection | *PLUS Num. obs: 27817 / Num. measured all: 89611 |
Reflection shell | *PLUS % possible obs: 68 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→60 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 714023.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED DATA CUTOFF HIGH (ABS(F)) : 714023.09 DATA CUTOFF LOW ( ABS(F)) : 0.000000
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Solvent computation | Solvent model: SHRINK MASK | SHELL MODEL / Bsol: 120 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→60 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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