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Yorodumi- PDB-5zlk: Mutation in the trinuclear site of CotA-laccase: H493A mutant, PH 8.0 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zlk | ||||||
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Title | Mutation in the trinuclear site of CotA-laccase: H493A mutant, PH 8.0 | ||||||
Components | Spore coat protein A | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Xie, T. / Liu, Z.C. / Wang, G.G. | ||||||
Citation | Journal: Chembiochem / Year: 2018 Title: Structural Insight into the Allosteric Coupling of Cu1 Site and Trinuclear Cu Cluster in CotA Laccase. Authors: Xie, T. / Liu, Z. / Wang, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zlk.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zlk.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zlk_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 5zlk_full_validation.pdf.gz | 452.4 KB | Display | |
Data in XML | 5zlk_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 5zlk_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/5zlk ftp://data.pdbj.org/pub/pdb/validation_reports/zl/5zlk | HTTPS FTP |
-Related structure data
Related structure data | 5zljC 5zllC 5zlmC 1gskS C: citing same article (ref.) 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: 58507.727 Da / Num. of mol.: 1 / Mutation: H493A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 / Gene: cotA, pig, BSU06300 / Production host: Escherichia coli (E. coli) / References: UniProt: P07788 | ||||||
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#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-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: 64.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30-43%(v/v) ethylene glycol, 100mM NaCl, 25mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 25601 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1gsk Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.49 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.357 / ESU R Free: 0.256 / 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: 36.34 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→30 Å
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Refine LS restraints |
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