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- PDB-4xsc: Complex structure of thymidylate synthase from varicella zoster v... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xsc | ||||||
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Title | Complex structure of thymidylate synthase from varicella zoster virus with a phosphorylated BVDU | ||||||
![]() | Thymidylate synthase | ||||||
![]() | TRANSFERASE / VZV / thymidylate synthase / herpesvirus | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / dihydrofolate reductase activity / methylation / cytosol Similarity search - Function | ||||||
Biological species | Varicella-zoster virus | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hew, K. | ||||||
![]() | ![]() Title: Structure of the Varicella Zoster Virus Thymidylate Synthase Establishes Functional and Structural Similarities as the Human Enzyme and Potentiates Itself as a Target of Brivudine. Authors: Hew, K. / Dahlroth, S.L. / Veerappan, S. / Pan, L.X. / Cornvik, T. / Nordlund, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.4 KB | Display | ![]() |
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PDB format | ![]() | 185.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 53 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xsdC ![]() 4xseSC 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: 35768.848 Da / Num. of mol.: 4 / Fragment: UNP residues 8-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Oka vaccine / Gene: ORF13 / Production host: ![]() ![]() #2: Chemical | ChemComp-BVP / ( #3: Chemical | ChemComp-1PE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8, 40% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 49296 / % possible obs: 96.2 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 1.9 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XSE Resolution: 2.901→29.706 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.45 / Stereochemistry target values: TWIN_LSQ_F
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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: 2.901→29.706 Å
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Refine LS restraints |
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LS refinement shell |
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