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Yorodumi- PDB-2cdy: Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cdy | ||||||
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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 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cdy.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cdy.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 2cdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cdy ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cdy | HTTPS FTP |
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-Related structure data
Related structure data | 2ce4SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 25982.875 Da / Num. of mol.: 4 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 | ChemComp-MN / #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE CRYSTALLISED CONTAINS AN N-TERMINAL PURIFICATION TAG. WHERE RESIDUES FROM THIS ARE ...THE SEQUENCE CRYSTALLIS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: DATA COMPLETENESS OF RANGE 41.2-2.25A IS 95.4% |
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-Data collection
Diffraction | Mean temperature: 100 K |
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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→41.2 Å / Num. obs: 48281 / % possible obs: 82.2 % / Redundancy: 9.4 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9 / % possible all: 41.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CE4 (MONOMER A) Resolution: 2→41.2 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.833 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO POOR ELECTRON DENSITY THE SIDE CHAINS OF THE FOLLOWING RESIDUES HAVE BEEN TRUNCATED AT CB LYS A142, LYS A210, GLU B46, ASP B105, GLN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO POOR ELECTRON DENSITY THE SIDE CHAINS OF THE FOLLOWING RESIDUES HAVE BEEN TRUNCATED AT CB LYS A142, LYS A210, GLU B46, ASP B105, GLN B91, LYS C210, LYS D139 DUE TO POOR ELECTRON DENSITY THE SIDE CHAIN OF GLU D158 HAS BEEN TRUNCATED AT CG. DUE TO POOR ELECTRON DENSITY THE SIDE CHAIN OF MET B23 HAS BEEN TRUNCATED AT SD. DUE TO POOR ELECTRON DENSITY THE SIDE CHAIN OF ASN C94 HAS BEEN TRUNCATED AT CA.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2→41.2 Å
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