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Yorodumi- PDB-7w6v: Crystal structure of a dicobalt-substituted small laccase at 2.47... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w6v | ||||||||||||
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Title | Crystal structure of a dicobalt-substituted small laccase at 2.47 angstrom | ||||||||||||
Components | Putative copper oxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / cobalt-binding / metalloenzyme | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Streptomyces coelicolor A3 | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | ||||||||||||
Authors | Yang, X. / Wu, F. / Wu, W. / Chen, X. / Fan, S. / Yu, P. / Mao, L. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Sci Adv / Year: 2022 Title: A versatile artificial metalloenzyme scaffold enabling direct bioelectrocatalysis in solution. Authors: Yang, X. / Wu, W. / Chen, X. / Wu, F. / Fan, S. / Yu, P. / Mao, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w6v.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w6v.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 7w6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w6v_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7w6v_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7w6v_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 7w6v_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/7w6v ftp://data.pdbj.org/pub/pdb/validation_reports/w6/7w6v | HTTPS FTP |
-Related structure data
Related structure data | 3cg8S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30608.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO6712 / Plasmid: pET20b / Production host: Escherichia coli #1/H766 (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9XAL8 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | 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: 7.68 Å3/Da / Density % sol: 83.99 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2% v/v PEG 400, 2.0 M ammonium sulfate, 100 mM HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jan 13, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.47→50 Å / Num. obs: 35302 / % possible obs: 100 % / Redundancy: 73.5 % / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.202 / Χ2: 0.78 / Net I/σ(I): 3.4 / Num. measured all: 2595911 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CG8 Resolution: 2.47→49.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.456 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 179.76 Å2 / Biso mean: 58.494 Å2 / Biso min: 35.53 Å2
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Refinement step | Cycle: final / Resolution: 2.47→49.43 Å
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LS refinement shell | Resolution: 2.47→2.531 Å / Rfactor Rfree error: 0
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