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- PDB-2ce4: Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ce4 | ||||||
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Title | Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans | ||||||
![]() | SUPEROXIDE DISMUTASE [MN] | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dennis, R. / Micossi, E. / McCarthy, J. / Moe, E. / Gordon, E. / Leonard, G. / McSweeney, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.7 KB | Display | ![]() |
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PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2cdyC ![]() 1vewS C: citing same article ( 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.995, -0.091, -0.043), Vector ![]() |
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Components
#1: Protein | Mass: 25982.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: R1 / Production host: ![]() ![]() ![]() ![]() #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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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.
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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
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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