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- PDB-8z59: The X-Ray crystal structure of multicopper oxidase from Sulfurimo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8z59 | ||||||
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Title | The X-Ray crystal structure of multicopper oxidase from Sulfurimonas sp. | ||||||
![]() | Bilirubin oxidase | ||||||
![]() | OXIDOREDUCTASE / oxidation / polyphenol | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y. / Qian, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: ESM-Ezy: a deep learning strategy for the mining of novel multicopper oxidases with superior properties. Authors: Qian, H. / Wang, Y. / Zhou, X. / Gu, T. / Wang, H. / Lyu, H. / Li, Z. / Li, X. / Zhou, H. / Guo, C. / Yuan, F. / Wang, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 711.6 KB | Display | ![]() |
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PDB format | ![]() | 585.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 13.6 MB | Display | ![]() |
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Full document | ![]() | 13.7 MB | Display | |
Data in XML | ![]() | 146.3 KB | Display | |
Data in CIF | ![]() | 189.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8z5bC ![]() 2fqgS S: Starting model for refinement 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
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Components
#1: Protein | Mass: 58260.406 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.96 % |
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Crystal grow | Temperature: 290.15 K / Method: liquid diffusion Details: 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→50 Å / Num. obs: 126901 / % possible obs: 96.5 % / Redundancy: 3.4 % / CC1/2: 0.984 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.58→2.62 Å / Num. unique obs: 126901 / Rrim(I) all: 14.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FQG Resolution: 2.58→39.52 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.74 / 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: 2.58→39.52 Å
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Refine LS restraints |
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LS refinement shell |
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