[English] 日本語
![](img/lk-miru.gif)
- PDB-1mmm: DISTINCT METAL ENVIRONMENT IN IRON-SUBSTITUTED MANGANESE SUPEROXI... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1mmm | ||||||
---|---|---|---|---|---|---|---|
Title | DISTINCT METAL ENVIRONMENT IN IRON-SUBSTITUTED MANGANESE SUPEROXIDE DISMUTASE PROVIDES A STRUCTURAL BASIS OF METAL SPECIFICITY | ||||||
![]() | PROTEIN (IRON-SUBSTITUTED MANGANESE SUPEROXIDE DISMUTASE) | ||||||
![]() | OXIDOREDUCTASE / IRON-SUBSTITUTED MANGANESE SUPEROXIDE DISMUTASE | ||||||
Function / homology | ![]() cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress ...cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress / protein homodimerization activity / DNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B. / Baker, E.N. | ||||||
![]() | Journal: J.Am.Chem.Soc. / Year: 1998 Title: Distinct Metal Environment in Fe-Substituted Manganese Superoxide Dismutase Provides a Structural Basis of Metal Specificity Authors: Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B. / Baker, E.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 97 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 421.8 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vewS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.729903, 0.132591, 0.670567), Vector: |
-
Components
#1: Protein | Mass: 22996.877 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.73 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.75 / Details: pH 8.75 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging dropDetails: Edwards, R.A., (1998) J. Biol. Inorg. Biol., 3, 161. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 15, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. obs: 20726 / % possible obs: 93.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.266 / % possible all: 82.6 |
Reflection | *PLUS Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 82.6 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1VEW Resolution: 2.2→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→100 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.3C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.3 |