[English] 日本語
Yorodumi- PDB-4oqm: Crystal structure of thymidine kinase from herpes simplex virus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oqm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ARA-EdU | ||||||
Components | Thymidine kinase | ||||||
Keywords | TRANSFERASE / DNA SYNTHESIS / THYMIDINE KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / 5-ETHYNYLURIDINE NUCLEOSIDE DERIVATIVE | ||||||
Function / homology | Function and homology information TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Pernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N. / Scapozza, L. | ||||||
Citation | Journal: To be Published Title: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ARA-EdU Authors: Pernot, L. / Neef, A.B. / Westermaier, Y. / Perozzo, R. / Luedtke, N. / Scapozza, L. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides. Authors: Neef, A.B. / Luedtke, N.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4oqm.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4oqm.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 4oqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oqm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4oqm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4oqm_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 4oqm_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/4oqm ftp://data.pdbj.org/pub/pdb/validation_reports/oq/4oqm | HTTPS FTP |
-Related structure data
Related structure data | 3f0tS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 35908.266 Da / Num. of mol.: 2 / Fragment: UNP residues 45-376 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Strain: 17 / Gene: TK, TK (UL23), UL23 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.9-1.2M LI2SO4, 1MM DTT, 0.1M HEPES PH 7.5-8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.1 Å / Num. all: 35059 / Num. obs: 35059 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 27.45 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.089 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4861 / Rsym value: 0.452 / % possible all: 93.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3F0T Resolution: 2.2→39.091 Å / SU ML: 0.21 / Isotropic thermal model: 30.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.49 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→39.091 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|