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Yorodumi- PDB-5lhl: Crystal Structure of Two-Domain Laccase from Streptomyces griseoflavus -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lhl | ||||||
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Title | Crystal Structure of Two-Domain Laccase 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 Å | ||||||
Authors | Gabdulkhakov, A.G. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of Two-Domain Laccase from Streptomyces griseoflavus Authors: Gabdulkhakov, A. / Tischenko, S. / Lisov, A. / Leontievsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lhl.cif.gz | 340.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lhl.ent.gz | 274.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/5lhl ftp://data.pdbj.org/pub/pdb/validation_reports/lh/5lhl | HTTPS FTP |
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-Related structure data
Related structure data | 3cg8S S: Starting model for refinement |
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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, 6 molecules ABCDEF
#1: Protein | Mass: 34751.637 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase |
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-Non-polymers , 5 types, 681 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | ChemComp-OXY / #5: Chemical | #6: 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: 1.99 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.3M NaCl, 0.01 M Tris-HCl 27,5 % (w/v) PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 118419 / % possible obs: 99.5 % / Redundancy: 3.66 % / Net I/σ(I): 9.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CG8 Resolution: 2→47.36 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→47.36 Å
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Refine LS restraints |
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LS refinement shell |
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