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- PDB-8p9u: Crystal Structure of Two-Domain Laccase mutant M199A/D268N from S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p9u | ||||||
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Title | Crystal Structure of Two-Domain Laccase mutant M199A/D268N from Streptomyces griseoflavus | ||||||
![]() | (Two-domain laccase) x 2 | ||||||
![]() | OXIDOREDUCTASE / Two-domain laccase / enzyme engineering / SgfSL / TNC / proton transport / laccase trinuclear cluster / oxygen reduction / structural biology | ||||||
Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kolyadenko, I.A. / Tishchenko, S.V. / Gabdulkhakov, A.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insight into the Amino Acid Environment of the Two-Domain Laccase's Trinuclear Copper Cluster. Authors: Kolyadenko, I. / Tishchenko, S. / Gabdulkhakov, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 352.6 KB | Display | ![]() |
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PDB format | ![]() | 281.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 8.6 MB | Display | ![]() |
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Full document | ![]() | 8.6 MB | Display | |
Data in XML | ![]() | 66.4 KB | Display | |
Data in CIF | ![]() | 95.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p9vC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 2 types, 6 molecules ABDEFC
#1: Protein | Mass: 30227.605 Da / Num. of mol.: 5 / Mutation: M199A/D268N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 30284.660 Da / Num. of mol.: 1 / Mutation: M199A/D268N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 785 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-OXY / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 5 Details: 15 % v/v PEG Smear High, 0.15 M Ammonium acetate, 0.1 M Sodium citrate condition #31 of BCS-1 from Molecular Dimensions, UK |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→23.54 Å / Num. obs: 104468 / % possible obs: 94.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 21.5 Å2 / CC1/2: 0.98 / Net I/σ(I): 8.01 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 10454 / CC1/2: 0.54 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→23.54 Å
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Refine LS restraints |
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LS refinement shell |
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