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- PDB-1iyz: Crystal Structures of the Quinone Oxidoreductase from Thermus the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iyz | ||||||
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Title | Crystal Structures of the Quinone Oxidoreductase from Thermus thermophilus HB8 and Its Complex with NADPH | ||||||
![]() | QUINONE OXIDOREDUCTASE | ||||||
![]() | OXIDOREDUCTASE / PROTEIN-NADPH COMPLEX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() NADPH:quinone reductase / : / NADPH:quinone reductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shimomura, Y. / Kakuta, Y. / Fukuyama, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal Structures of the Quinone Oxidoreductase from Thermus thermophilus HB8 and Its Complex with NADPH: Implication for NADPH and Substrate Recognition Authors: Shimomura, Y. / Kakuta, Y. / Fukuyama, K. #1: ![]() Title: Overproduction, crystallization and preliminary X-ray diffraction analysis of a quinone oxidoreductase from Thermus thermophilus HB8 Authors: Shimomura, Y. / Sumiguchi-Agari, K. / Masui, R. / Kuramitsu, S. / Fukuyama, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.2 KB | Display | ![]() |
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PDB format | ![]() | 49.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.6 KB | Display | ![]() |
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Full document | ![]() | 783.1 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32126.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NDP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.56 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.9 Details: ammonium dihydrogen phosphate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 8 / Method: vapor diffusion, hanging dropDetails: Shimomura, Y., (2002) Acta Crystallogr.,Sect.D, 58, 1365. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 29, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 278044 / Num. obs: 278044 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.5 Å2 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 11091 / Num. measured all: 278044 / Rmerge(I) obs: 0.116 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.205 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.738 Å2 / ksol: 0.37952 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→44.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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