[English] 日本語
Yorodumi- PDB-8ile: The crystal structure of dGTPalphaSe-Rp:DNApre-II:Pol X substrate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ile | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The crystal structure of dGTPalphaSe-Rp:DNApre-II:Pol X substrate ternary complex | |||||||||||||||
Components |
| |||||||||||||||
Keywords | REPLICATION/DNA / DNA polymerase / substrate complex / selenium-modified dNTP / configuration / REPLICATION-DNA complex | |||||||||||||||
Function / homology | Function and homology information virion component / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | African swine fever virus synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||||||||
Authors | Qin, T. / Gan, J.H. / Huang, Z. | |||||||||||||||
Funding support | China, 4items
| |||||||||||||||
Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom. Authors: Qin, T. / Hu, B. / Zhao, Q. / Wang, Y. / Wang, S. / Luo, D. / Lyu, J. / Chen, Y. / Gan, J. / Huang, Z. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ile.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ile.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ile.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/8ile ftp://data.pdbj.org/pub/pdb/validation_reports/il/8ile | HTTPS FTP |
---|
-Related structure data
Related structure data | 8ildC 8ilfC 8ilgC 8ilhC 8iliC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20465.592 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus (strain Badajoz 1971 Vero-adapted) Gene: Ba71V-97, O174L / Production host: Escherichia coli (E. coli) / References: UniProt: P42494, DNA-directed DNA polymerase #2: DNA chain | Mass: 2715.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-MN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.05 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M L-proline, HEPES pH 8.6 (0.1 M),10% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 18, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→30 Å / Num. obs: 10889 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.117 / Χ2: 0.216 / Net I/σ(I): 7.8 / Num. measured all: 138097 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.74 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.857 / SU B: 38.321 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.522 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3→29.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|