+Open data
-Basic information
Entry | Database: PDB / ID: 5a9g | ||||||
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Title | Manganese Superoxide Dismutase from Sphingobacterium sp. T2 | ||||||
Components | MANGANESE SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE / LIGNIN VALORISATION / LIGNIN OXIDATION / MANGANESE SUPEROXIDE DISMUTASE / SPHINGOBACTERIUM | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | SPHINGOBACTERIUM SPIRITIVORUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Rashid, G.M.M. / Taylor, C.R. / Liu, Y. / Zhang, X. / Rea, D. / Fulop, V. / Bugg, T.D.H. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Identification of Manganese Superoxide Dismutase from Sphingobacterium Sp. T2 as a Novel Bacterial Enzyme for Lignin Oxidation. Authors: Rashid, G.M. / Taylor, C.R. / Liu, Y. / Zhang, X. / Rea, D. / Fulop, V. / Bugg, T.D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a9g.cif.gz | 176.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a9g.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 5a9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a9g_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 5a9g_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 5a9g_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 5a9g_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/5a9g ftp://data.pdbj.org/pub/pdb/validation_reports/a9/5a9g | HTTPS FTP |
-Related structure data
Related structure data | 2rcvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26429.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SPHINGOBACTERIUM SPIRITIVORUM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL50*PLUS, superoxide dismutase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 20% (W/V) PEG 3350, 0.2 M DI-AMMONIUM HYDROGEN CITRATE, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2014 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→37 Å / Num. obs: 87001 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.35→1.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / % possible all: 79 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RCV Resolution: 1.35→36.6 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.307 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED
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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: 14.463 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→36.6 Å
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Refine LS restraints |
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