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- PDB-5a12: Crystal structure of Chlorite Dismutase from Magnetospirillum sp.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a12 | ||||||
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Title | Crystal structure of Chlorite Dismutase from Magnetospirillum sp. in complex with azide | ||||||
![]() | CHLORITE DISMUTASE | ||||||
![]() | OXIDOREDUCTASE / CHLORITE / CHLORIDE / DETOXIFICATION / HEME / IRON | ||||||
Function / homology | ![]() chlorite O2-lyase / chlorite O2-lyase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Correia, H.D. / Santos-Silva, T. | ||||||
![]() | ![]() Title: Ligand Binding to Chlorite Dismutase from Magnetospirillum Sp. Authors: De Schutter, A. / Correia, H. / Freire, D.M. / Rivas, M.G. / Rizzi, A.C. / Santos-Silva, T. / Gonzalez, P.J. / Van Doorslaer, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 564.2 KB | Display | ![]() |
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PDB format | ![]() | 467.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 66.6 KB | Display | |
Data in CIF | ![]() | 98.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a13C ![]() 3q08S 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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Unit cell |
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Components
#1: Protein | Mass: 26806.664 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-AZI / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.7 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 16% PEG 6000, 0.01M SODIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.84 Å / Num. obs: 268333 / % possible obs: 98.4 % / Observed criterion σ(I): 1.4 / Redundancy: 3.8 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.4 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3Q08 Resolution: 1.4→71.44 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 2.076 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→71.44 Å
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Refine LS restraints |
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