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Yorodumi- PDB-4yvu: Crystal structure of CotA native enzyme in the acid condition, PH5.6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yvu | ||||||
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Title | Crystal structure of CotA native enzyme in the acid condition, PH5.6 | ||||||
Components | Spore coat protein A | ||||||
Keywords | OXIDOREDUCTASE / Spore coat protein A / laccase | ||||||
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: 2.3 Å | ||||||
Authors | Liu, Z.C. / Xie, T. / Wang, G.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site Authors: Liu, Z. / Xie, T. / Zhong, Q. / Wang, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yvu.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yvu.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 4yvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yvu_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 4yvu_full_validation.pdf.gz | 443.1 KB | Display | |
Data in XML | 4yvu_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 4yvu_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/4yvu ftp://data.pdbj.org/pub/pdb/validation_reports/yv/4yvu | HTTPS FTP |
-Related structure data
Related structure data | 4yvnC 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: 58574.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: cotA, pig, BSU06300 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P07788 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30-42%(v/v) ethylene glycol,100mM sodium citrate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.4 Å / Num. obs: 36605 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GSK Resolution: 2.3→29.38 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.773 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.158 / 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: 21.344 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→29.38 Å
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