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- PDB-6k8p: Structural and catalytic analysis of two diverse uridine phosphor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k8p | |||||||||
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Title | Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici. | |||||||||
![]() | Uridine phosphorylase | |||||||||
![]() | TRANSFERASE / uridine phosphorylase / phytophthora capsici / thymidine | |||||||||
Function / homology | ![]() uridine phosphorylase / uridine catabolic process / uridine phosphorylase activity / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yang, C.C. / Zhang, X.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and catalytic analysis of two diverse uridine phosphorylases in Phytophthora capsici. Authors: Yang, C. / Li, J. / Huang, Z. / Zhang, X. / Gao, X. / Zhu, C. / Morris, P.F. / Zhang, X. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 424 KB | Display | ![]() |
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PDB format | ![]() | 350.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 54.1 KB | Display | |
Data in CIF | ![]() | 74.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k5gSC ![]() 6k5hC ![]() 6k5kC 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
-Protein / Sugars , 2 types, 6 molecules ABCD![](data/chem/img/R1P.gif)
![](data/chem/img/R1P.gif)
#1: Protein | Mass: 33151.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: thymidine Source: (gene. exp.) ![]() Gene: up / Production host: ![]() ![]() #4: Sugar | |
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-Non-polymers , 4 types, 590 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/THM.gif)
![](data/chem/img/TDR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/THM.gif)
![](data/chem/img/TDR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #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: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: PEG 4000, potassium phosphate, magenesium chloride, cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 87357 / % possible obs: 99.7 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.96→2.03 Å / Rmerge(I) obs: 0.984 / Num. unique obs: 8200 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6K5G Resolution: 1.965→38.463 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.2 Å2 / Biso mean: 32.5664 Å2 / Biso min: 7.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.965→38.463 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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