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- PDB-7pes: Crystal Structure of Two-Domain Laccase mutant M199G from Strepto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pes | ||||||
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Title | Crystal Structure of Two-Domain Laccase mutant M199G from Streptomyces griseoflavus | ||||||
![]() | Two-domain laccase | ||||||
![]() | OXIDOREDUCTASE / Two-Domain Laccase / laccase / Streptomyces griseoflavus | ||||||
Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gabdulkhakov, A. / Tishchenko, S. / Kolyadenko, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Engineering the Catalytic Properties of Two-Domain Laccase from Streptomyces griseoflavus Ac-993. Authors: Kolyadenko, I. / Scherbakova, A. / Kovalev, K. / Gabdulkhakov, A. / Tishchenko, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 428.5 KB | Display | ![]() |
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PDB format | ![]() | 280 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 499.3 KB | Display | ![]() |
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Full document | ![]() | 508.7 KB | Display | |
Data in XML | ![]() | 64.9 KB | Display | |
Data in CIF | ![]() | 93.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7penC ![]() 7pfrC ![]() 7ptmC ![]() 7pu0C ![]() 7puhC ![]() 5lhlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30819.178 Da / Num. of mol.: 6 / Mutation: M199G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-NA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.46 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 15 % v/v PEG Smear High, 0.15 M Ammonium acetate, 0.1 M Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977175 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48 Å / Num. obs: 168209 / % possible obs: 99.9 % / Redundancy: 6.83 % / Biso Wilson estimate: 34.5 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.066 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 12404 / CC1/2: 0.502 / Rrim(I) all: 1.86 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LHL Resolution: 1.75→47.18 Å / SU ML: 0.2253 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4629 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: 38.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→47.18 Å
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Refine LS restraints |
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LS refinement shell |
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