[English] 日本語
![](img/lk-miru.gif)
- PDB-4yip: X-ray structure of the iron/manganese cambialistic superoxide dis... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4yip | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the iron/manganese cambialistic superoxide dismutase from Streptococcus mutans | ||||||
![]() | Superoxide dismutase [Mn/Fe] | ||||||
![]() | OXIDOREDUCTASE / cambialistic | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Russo Krauss, I. / Merlino, A. / Pica, A. / Sica, F. | ||||||
![]() | ![]() Title: Fine tuning of metal-specific activity in the Mn-like group of cambialistic superoxide dismutases Authors: Russo Krauss, I. / Merlino, A. / Pica, A. / Rullo, R. / Bertoni, A. / Capasso, A. / Amato, M. / Riccitiello, F. / De Vendittis, E. / Sica, F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 172.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 137.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 416.1 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yioC ![]() 3lioS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23590.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 28-33% PEG 8000, 0.1 M sodium cacodylate buffer at pH 6.0, 3% acetonitrile |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 43458 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3LIO Resolution: 2.15→31.39 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.424 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.367 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→31.39 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|