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- PDB-6gsc: Sphingobacterium sp. T2 manganese superoxide dismutase catalyses ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gsc | ||||||||||||
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Title | Sphingobacterium sp. T2 manganese superoxide dismutase catalyses the oxidative demethylation of polymeric lignin via generation of hydroxyl radical | ||||||||||||
![]() | (Superoxide dismutase) x 2 | ||||||||||||
![]() | OXIDOREDUCTASE / LIGNIN VALORISATION / LIGNIN OXIDATION / MANGANESE KEYWDS 2 SUPEROXIDE DISMUTASE / SPHINGOBACTERIUM | ||||||||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Rashid, G.M.M. / Zhang, X. / Wilkinson, R.C. / Fulop, V. / Cottyn, B. / Baumberger, S. / Bugg, T.D.H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Sphingobacterium sp. T2 Manganese Superoxide Dismutase Catalyzes the Oxidative Demethylation of Polymeric Lignin via Generation of Hydroxyl Radical. Authors: Rashid, G.M.M. / Zhang, X. / Wilkinson, R.C. / Fulop, V. / Cottyn, B. / Baumberger, S. / Bugg, T.D.H. #1: ![]() 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. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.1 KB | Display | ![]() |
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PDB format | ![]() | 81 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.6 KB | Display | ![]() |
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Full document | ![]() | 422.6 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gsbC ![]() 5a9gS 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: 22908.562 Da / Num. of mol.: 1 / Mutation: A31H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() | ||
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#2: Protein | Mass: 23037.744 Da / Num. of mol.: 1 / Mutation: A31H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37 % / Description: rod shape |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 130 mM ammonium citrate, 26% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2018 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→40 Å / Num. obs: 94757 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Rrim(I) all: 0.093 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.32→1.39 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 2 / Num. unique obs: 6973 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5a9g Resolution: 1.32→39.66 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.756 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.046 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.911 Å2
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Refinement step | Cycle: 1 / Resolution: 1.32→39.66 Å
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Refine LS restraints |
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