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Yorodumi- PDB-4akq: Mutations in the neighbourhood of CotA-laccase trinuclear site: E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4akq | ||||||
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Title | Mutations in the neighbourhood of CotA-laccase trinuclear site: E498D mutant | ||||||
Components | SPORE COAT PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / COTA-LACCASE / MULTI-COPPER OXIDASE / TRINUCLEAR CLUSTER / OXYGEN REDUCTION | ||||||
Function / homology | Function and homology information bilirubin oxidase / laccase / sporulation resulting in formation of a cellular spore / outer membrane-bounded periplasmic space / oxidoreductase activity / copper ion binding Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Silva, C.S. / Chen, Z. / Durao, P. / Pereira, M.M. / Todorovic, S. / Hildebrandt, P. / Martins, L.O. / Lindley, P.F. / Bento, I. | ||||||
Citation | Journal: Dalton Trans / Year: 2010 Title: The Role of Glu498 in the Dioxygen Reactivity of Cota-Laccase from Bacillus Subtilis. Authors: Chen, Z. / Durao, P. / Silva, C.S. / Pereira, M.M. / Todorovic, S. / Hildebrandt, P. / Bento, I. / Lindley, P.F. / Martins, L.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4akq.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4akq.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 4akq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/4akq ftp://data.pdbj.org/pub/pdb/validation_reports/ak/4akq | HTTPS FTP |
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-Related structure data
Related structure data | 4akoC 4akpC 1w6lS S: Starting model for refinement C: citing same article (ref.) |
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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: 58560.766 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ETHYLENE GLYCOL (EDO) AS SOLVENT / Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07788, laccase | ||||||||
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#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-OXY / | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.3 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 10% PEG 4K, 0.1 M SODIUM CITRATE PH 5.5, 26% ISOPROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→54.07 Å / Num. obs: 48362 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W6L Resolution: 2.1→40.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.25 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.SYSTEMATICALLY DISORDERED REGION BETWEEN RESIDUES 212 AND 215. LOOP REGION BETWEEN RESIDUES 89 AND 97 POORLY DEFINED.
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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: 27.252 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40.82 Å
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Refine LS restraints |
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