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- PDB-1do6: CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE OXIDIZED STATE A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1do6 | ||||||
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Title | CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE OXIDIZED STATE AT 2.0 ANGSTROM RESOLUTION | ||||||
![]() | SUPEROXIDE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / NON-HEME IRON PROTEIN / IMMUNOGLOBULIN-LIKE (IG) BETA BARREL FOLD | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Yeh, A.P. / Hu, Y. / Jenney Junior, F.E. / Adams, M.W. / Rees, D.C. | ||||||
![]() | ![]() Title: Structures of the superoxide reductase from Pyrococcus furiosus in the oxidized and reduced states. Authors: Yeh, A.P. / Hu, Y. / Jenney Jr., F.E. / Adams, M.W. / Rees, D.C. #1: ![]() Title: Anaerobic Microbes: Oxygen Detoxification Without Superoxide Dismutase Authors: Jenney Junior, F.E. / Verhagen, M.F. / Cui, X. / Adams, M.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 47.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.4 KB | Display | ![]() |
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Full document | ![]() | 368.9 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 9.3 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 on special symmetry positions |
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Components
#1: Protein | Mass: 14344.189 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.57 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG4000, TRIS-HYDROCHLORIDE, PH 8.0, GLYCEROL, SODIUM CHLORIDE, ETHANOL, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: Mar 21, 1997 |
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→28.8 Å / Num. all: 16334 / Num. obs: 16334 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.178 / % possible all: 84.2 |
Reflection | *PLUS Num. measured all: 65376 |
Reflection shell | *PLUS % possible obs: 84.2 % / Mean I/σ(I) obs: 4.4 |
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Processing
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Refinement | Resolution: 2→28.8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→28.8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 28.8 Å / σ(F): 0 / % reflection Rfree: 6.4 % / Rfactor obs: 0.16 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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