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- PDB-1dqi: CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE FROM P. FURIOSUS IN THE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dqi | ||||||
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Title | CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE FROM P. FURIOSUS IN THE OXIDIZED STATE AT 1.7 ANGSTROMS 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 Jr., F.E. / Adams, M.W.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 Jr., F.E. / Verhagen, M.F. / Cui, X. / Adams, M.W.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 | ![]() | 120.2 KB | Display | ![]() |
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PDB format | ![]() | 93.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376.4 KB | Display | ![]() |
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Full document | ![]() | 379 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 17.7 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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Unit cell |
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Components
#1: Protein | Mass: 14344.189 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | Compound details | This structure of oxidized SOR is different from the 2.0 Angstroms resolution structure of oxidized ...This structure of oxidized SOR is different from the 2.0 Angstroms resolution structure of oxidized SOR in that the data set for this structure was collected under cryogenic temperatures and is at a higher resolution of 1.7 Angstroms | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 13, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.6 Å / Num. all: 51080 / Num. obs: 51080 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.251 / Num. unique all: 2506 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 222107 |
Reflection shell | *PLUS % possible obs: 99.8 % / Mean I/σ(I) obs: 5.5 |
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Processing
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Refinement | Resolution: 1.7→29.6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→29.6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 29.6 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.203 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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