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Yorodumi- PDB-5o4q: Crystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o4q | ||||||
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Title | Crystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase from Streptomyces griseoflavus with 0.25 mM copper sulfate on growth medium | ||||||
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: 1.9 Å | ||||||
Authors | Gabdulkhakov, A.G. / Tishchenko, T.V. | ||||||
Citation | Journal: Mol.Biol.(Moscow) / Year: 2018 Title: Incorporation of Copper Ions into T2/T3 Centers of Two-Domain Laccases. Authors: Gabdulkhakov, A.G. / Kostareva, O.S. / Kolyadenko, I.A. / Mikhaylina, A.O. / Trubitsina, L.I. / Tishchenko, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o4q.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5o4q.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 5o4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/5o4q ftp://data.pdbj.org/pub/pdb/validation_reports/o4/5o4q | HTTPS FTP |
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-Related structure data
Related structure data | 5o3kSC 5o4iC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 34697.523 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: mutations M54L, M64L, M96L / Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase |
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-Non-polymers , 7 types, 784 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | ChemComp-AZI / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-FMT / | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
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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: 2.04 Å3/Da / Density % sol: 39.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 23% PEG 4000, 0.05M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 235821 / % possible obs: 95.69 % / Redundancy: 3.4 % / Net I/σ(I): 6.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O3K Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.541 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R Free: 0.14
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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: 30.373 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→50 Å
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Refine LS restraints |
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