+Open data
-Basic information
Entry | Database: PDB / ID: 5h38 | |||||||||
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Title | Structural analysis of KSHV thymidylate synthase | |||||||||
Components | ORF70 | |||||||||
Keywords | TRANSFERASE / thymidylate synthase / inhibitor / raltitrexed / dUMP | |||||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / dihydrofolate reductase activity / methylation / cytosol Similarity search - Function | |||||||||
Biological species | Human herpesvirus 8 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Choi, Y.M. / Yeo, H.K. / Park, Y.W. / Lee, J.Y. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: PLoS ONE / Year: 2016 Title: Structural Analysis of Thymidylate Synthase from Kaposi's Sarcoma-Associated Herpesvirus with the Anticancer Drug Raltitrexed. Authors: Choi, Y.M. / Yeo, H.K. / Park, Y.W. / Lee, J.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h38.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h38.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 5h38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/5h38 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/5h38 | HTTPS FTP |
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-Related structure data
Related structure data | 5h39C 5h3aC 1hvyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32749.492 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 51-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF70 / Production host: Escherichia coli (E. coli) / References: UniProt: F5HBQ9, UniProt: P90463*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: potassium phosphate (monobasic), PEG 8K, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.695→50 Å / Num. obs: 65947 / % possible obs: 99.2 % / Redundancy: 4.9 % / Net I/σ(I): 36.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.8 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HVY Resolution: 1.7→19.827 Å / FOM work R set: 0.8826 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.46 / Phase error: 18.97 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.74 Å2 / Biso mean: 24.89 Å2 / Biso min: 9.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→19.827 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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