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Yorodumi- PDB-4akp: Mutations in the neighbourhood of CotA-laccase trinuclear site: E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4akp | ||||||
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Title | Mutations in the neighbourhood of CotA-laccase trinuclear site: E498T mutant | ||||||
Components | SPORE COAT PROTEIN A | ||||||
Keywords | OXIDOREDUCTASE / 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 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 | 4akp.cif.gz | 128.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4akp.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 4akp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4akp_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 4akp_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 4akp_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 4akp_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/4akp ftp://data.pdbj.org/pub/pdb/validation_reports/ak/4akp | HTTPS FTP |
-Related structure data
Related structure data | 4akoC 4akqC 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: 58562.781 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-OXY / | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | AT RESIDUE 35 THERE IS AN OXIDIZED CYSTEINE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.4 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 8 % PEG 4K, 0.1 M SODIUM CITRATE PH5.5, 26 % ISOPROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→88.39 Å / Num. obs: 55879 / % possible obs: 99.6 % / Observed criterion σ(I): 2.2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.35 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W6L Resolution: 2→44.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.129 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.649 Å2
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Refinement step | Cycle: LAST / Resolution: 2→44.11 Å
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Refine LS restraints |
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