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Yorodumi- PDB-6zip: Crystal Structure of Two-Domain Laccase mutant R240A from Strepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zip | |||||||||
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Title | Crystal Structure of Two-Domain Laccase mutant R240A from Streptomyces griseoflavus | |||||||||
Components | Two-domain laccase | |||||||||
Keywords | OXIDOREDUCTASE / Two-Domain Laccase / laccase / Streptomyces griseoflavus | |||||||||
Function / homology | Function and homology information hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding Similarity search - Function | |||||||||
Biological species | Streptomyces griseoflavus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Gabdulkhakov, A.G. / Tishchenko, T.V. / Kolyadenko, I.A. | |||||||||
Funding support | Russian Federation, 2items
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Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2022 Title: The role of positive charged residue in the proton-transfer mechanism of two-domain laccase from Streptomyces griseoflavus Ac-993. Authors: Gabdulkhakov, A. / Kolyadenko, I. / Oliveira, P. / Tamagnini, P. / Mikhaylina, A. / Tishchenko, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zip.cif.gz | 661.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zip.ent.gz | 533.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/6zip ftp://data.pdbj.org/pub/pdb/validation_reports/zi/6zip | HTTPS FTP |
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-Related structure data
Related structure data | 6zijC 5lhlS 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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Unit cell |
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-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 34665.523 Da / Num. of mol.: 12 / Mutation: R240A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase |
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-Non-polymers , 5 types, 847 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PER / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.53 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 9.3 / Details: 20 % v/v PEG Smear High 0.1 M Bicine, pH 9.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.861 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.861 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 200840 / % possible obs: 97.6 % / Redundancy: 2.67 % / Biso Wilson estimate: 35.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.09 |
Reflection shell | Resolution: 2.05→2.1 Å / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 14801 / CC1/2: 0.69 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LHL Resolution: 2.05→47.4 Å / SU ML: 0.2382 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.6624 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→47.4 Å
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Refine LS restraints |
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LS refinement shell |
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