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Yorodumi- PDB-4a66: Mutations in the neighbourhood of CotA-laccase trinuclear site: D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a66 | ||||||
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Title | Mutations in the neighbourhood of CotA-laccase trinuclear site: D116A mutant | ||||||
Components | SPORE COAT PROTEIN A | ||||||
Keywords | OXIDOREDUCTASE / MULTI-COPPER OXIDASE / OXIDOREDUCTASE ACTIVITY / TRINUCLEAR CLUSTER / DIOXYGEN 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Silva, C.S. / Lindley, P.F. / Bento, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: The Role of Asp116 in the Reductive Cleavage of Dioxygen to Water in Cota Laccase: Assistance During the Proton Transfer Mechanism Authors: Silva, C.S. / Damas, J.M. / Chen, Z. / Brissos, V. / Martins, L.O. / Soares, C.M. / Lindley, P.F. / Bento, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a66.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a66.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 4a66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/4a66 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a66 | HTTPS FTP |
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-Related structure data
Related structure data | 4a67C 4a68C 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: 58530.781 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source 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-EDO / #4: Chemical | ChemComp-PER / | #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: 3.49 Å3/Da / Density % sol: 64.76 % / Description: NONE |
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Crystal grow | pH: 7.6 / Details: 35% ETHYLENE GLYCOL, pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.544 |
Detector | Type: BRUKER PT135 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.544 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→24.68 Å / Num. obs: 60037 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W6L Resolution: 1.95→19.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.53 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. SYSTEMATICALLY DISORDERED REGION BETWEEN RESIDUES 212 AND 215. LOOP REGION BETWEEN RESIDUES 89 AND 97 POORLY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. SYSTEMATICALLY DISORDERED REGION BETWEEN RESIDUES 212 AND 215. LOOP REGION BETWEEN RESIDUES 89 AND 97 POORLY DEFINED. NON MODELLED MODIFIED TYR 358 AT POSITION CD2. MISSING LOOP COMPRISING RESIDUES 360-363.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.99 Å
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Refine LS restraints |
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