[English] 日本語
Yorodumi- PDB-2ce4: Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ce4 | ||||||
---|---|---|---|---|---|---|---|
Title | Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans | ||||||
Components | SUPEROXIDE DISMUTASE [MN] | ||||||
Keywords | OXIDOREDUCTASE / MANGANESE SUPEROXIDE DISMUTASE / DEINOCOCCUS RADIODURANS / RADIATION RESISTANCE | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dennis, R. / Micossi, E. / McCarthy, J. / Moe, E. / Gordon, E. / Leonard, G. / McSweeney, S. | ||||||
Citation | Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2006 Title: Structure of the manganese superoxide dismutase from Deinococcus radiodurans in two crystal forms. Authors: Dennis, R.J. / Micossi, E. / McCarthy, J. / Moe, E. / Gordon, E.J. / Kozielski-Stuhrmann, S. / Leonard, G.A. / McSweeney, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ce4.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ce4.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ce4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/2ce4 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/2ce4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2cdyC 1vewS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.995, -0.091, -0.043), Vector: |
-Components
#1: Protein | Mass: 25982.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Strain: R1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9RUV2, superoxide dismutase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE CRYSTALLISED CONTAINS AN N-TERMINAL PURIFICATION TAG. WHERE RESIDUES FROM THIS ARE ...THE SEQUENCE CRYSTALLIS | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % |
---|---|
Crystal grow | pH: 8.5 / Details: 10 MM TRIS-HCL PH 8.5, 20MM MNCL2, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.4 Å / Num. obs: 20567 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 6 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VEW Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.144 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELECTRON DENSITY FOR RESIDUES A90-A95 AND B91-B95 IS POOR. THEY ARE NOT INCLUDED IN THE MODEL.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.34 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|