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- PDB-1p7g: Crystal structure of superoxide dismutase from Pyrobaculum aerophilum -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p7g | ||||||
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Title | Crystal structure of superoxide dismutase from Pyrobaculum aerophilum | ||||||
![]() | Superoxide dismutase | ||||||
![]() | OXIDOREDUCTASE / ALPHA-BETA | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, S. / Sawaya, M.R. / Eisenberg, D. | ||||||
![]() | ![]() Title: Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning. Authors: Lee, S. / Sawaya, M.R. / Eisenberg, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 868.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 680.4 KB | Display | ![]() |
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Full document | ![]() | 823.6 KB | Display | |
Data in XML | ![]() | 216.2 KB | Display | |
Data in CIF | ![]() | 288.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sss ![]() 1iks S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a tetramer. There are six tetramers in the asymmetric unit. |
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Components
#1: Protein | Mass: 25651.740 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-BME / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3000, calcium acetate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 1999 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→36.51 Å / Num. all: 476704 / Num. obs: 465126 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.1 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3.3 / Num. unique all: 39384 / % possible all: 82.6 | |||||||||||||||
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 36.4 Å / Num. measured all: 2013670 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 82.6 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SSS ![]() 1sss Resolution: 1.8→36.45 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Partial twinning incorporated with the twinning fraction being 0.463.
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Displacement parameters | Biso mean: 21 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→36.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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Refinement | *PLUS Highest resolution: 1.8 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.263 / Rfactor Rwork: 0.241 |