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- PDB-7azr: Crystal structure of the iron/manganese cambialistic superoxide d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7azr | ||||||
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Title | Crystal structure of the iron/manganese cambialistic superoxide dismutase from Rhodobacter capsulatus complex with Mn | ||||||
![]() | Superoxide dismutase [Fe] | ||||||
![]() | OXIDOREDUCTASE / superoxide oxidoreductase / SODs / metal ion binding protein. | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ponce-Salvatierra, A. / Hermoso, J.A. | ||||||
![]() | ![]() Title: Structural and functional characterization of the cambialistic superoxide dismutase from Rhodobacter capsulatus. Authors: Ponce-Salvatierra, A. / Di Capua, C. / Gonzalez, J. / Cortez, N. / Hermoso, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.6 KB | Display | ![]() |
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PDB format | ![]() | 136.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.9 KB | Display | ![]() |
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Full document | ![]() | 432.2 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7azqC ![]() 1dt0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22016.709 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 58% MPD, 200 mM CaCl2, and 100 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97909 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.15 Å / Num. obs: 35121 / % possible obs: 99.98 % / Redundancy: 34.8 % / CC1/2: 0.999 / Net I/σ(I): 26.24 |
Reflection shell | Resolution: 2.1→2.175 Å / Mean I/σ(I) obs: 3.54 / Num. unique obs: 3405 / CC1/2: 0.881 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1dt0 Resolution: 2.1→45.15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.263 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.742 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→45.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.153 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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