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Yorodumi- PDB-4yvn: Crystal structure of CotA laccase complexed with ABTS at a novel ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yvn | ||||||
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Title | Crystal structure of CotA laccase complexed with ABTS at a novel binding site | ||||||
Components | Spore coat protein A | ||||||
Keywords | OXIDOREDUCTASE / Spore coat protein A / Laccase / ABTS | ||||||
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 | 4yvn.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yvn.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 4yvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/4yvn ftp://data.pdbj.org/pub/pdb/validation_reports/yv/4yvn | HTTPS FTP |
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-Related structure data
Related structure data | 4yvuC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 404 molecules
#2: Chemical | #3: Chemical | ChemComp-EBS / | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.66 % |
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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: 36864 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 6.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GSK Resolution: 2.3→29.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.711 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.164 / 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: 22.07 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→29.4 Å
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Refine LS restraints |
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