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Yorodumi- PDB-6vox: Crystal structure of multi-copper oxidase from Pseudomonas Parafulva -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vox | ||||||||||||
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Title | Crystal structure of multi-copper oxidase from Pseudomonas Parafulva | ||||||||||||
Components | Copper oxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / LACCASE / COPPER OXIDASE / ACOUSTIC DROPLET EJECTION / LIGNIN | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Pseudomonas parafulva (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||||||||
Authors | Partowmah, S.H. / Coler, E.A. / Soares, A.S. / Collins, R.E. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Crystal structure of multi-copper oxidase from Pseudomonas Parafulva Authors: Partowmah, S. / Coler, E.A. / Soares, A.S. / Collins, R.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vox.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vox.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 6vox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/6vox ftp://data.pdbj.org/pub/pdb/validation_reports/vo/6vox | HTTPS FTP |
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-Related structure data
Related structure data | 6vowS 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: 47293.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas parafulva (bacteria) / Gene: NJ69_01745 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7JLK4 | ||
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#2: Chemical | ChemComp-C2O / | ||
#3: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.8 Å3/Da / Density % sol: 78.8 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 9 Details: Crystallized in plastic sitting drop trays, 30 nl of protein (concentration 10 mg/mL) combined with 30 nl precipitant: 0.0425 M BICINE pH 9.0 0.0425 M Sodium chloride 8.5% v/v Polyethylene ...Details: Crystallized in plastic sitting drop trays, 30 nl of protein (concentration 10 mg/mL) combined with 30 nl precipitant: 0.0425 M BICINE pH 9.0 0.0425 M Sodium chloride 8.5% v/v Polyethylene glycol monomethyl ether 550 7.5% v/v Glycerol Solution was equilibrated against a reservoir of 60% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9202 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 10690 / % possible obs: 92.3 % / Redundancy: 29.33 % / CC1/2: 0.997 / Rmerge(I) obs: 0.29 / Net I/σ(I): 8.38 |
Reflection shell | Resolution: 3.8→3.9 Å / Rmerge(I) obs: 2.578 / Num. unique obs: 635 / CC1/2: 0.258 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VOW Resolution: 3.8→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.931 / SU B: 51.885 / SU ML: 0.6 / Cross valid method: THROUGHOUT / ESU R Free: 0.596 / 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: 195.234 Å2
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Refinement step | Cycle: 1 / Resolution: 3.8→30 Å
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Refine LS restraints |
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