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- PDB-6kd3: 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: 6kd3 | ||||||
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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 | ||||||
Function / homology | Nucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, C.C. / Zhang, X.G. | ||||||
![]() | ![]() Title: Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici. Authors: Yang, C.C. / Zhang, X.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.8 KB | Display | ![]() |
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PDB format | ![]() | 84.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.6 KB | Display | ![]() |
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Full document | ![]() | 465.1 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34856.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT1534 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium iodide, 20% PEG 3350 |
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-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: Jun 3, 2019 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→50 Å / Num. obs: 31606 / % possible obs: 82 % / Redundancy: 4 % / Rmerge(I) obs: 0.235 / Net I/σ(I): 6.39 |
Reflection shell | Resolution: 2.76→2.86 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1242 / % possible all: 84.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.77 Å2 / Biso mean: 32.1619 Å2 / Biso min: 3.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.764→47.45 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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