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Yorodumi- PDB-8ili: The crystal structure of dG(Se-Rp)-DNA:Pol X product binary complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ili | |||||||||||||||
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Title | The crystal structure of dG(Se-Rp)-DNA:Pol X product binary complex | |||||||||||||||
Components |
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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: 1.9 Å | |||||||||||||||
Authors | Qin, T. / Gan, J.H. / Huang, Z. | |||||||||||||||
Funding support | China, 4items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ili.cif.gz | 193.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ili.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 8ili.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ili_validation.pdf.gz | 495.7 KB | Display | wwPDB validaton report |
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Full document | 8ili_full_validation.pdf.gz | 499.8 KB | Display | |
Data in XML | 8ili_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 8ili_validation.cif.gz | 53.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/8ili ftp://data.pdbj.org/pub/pdb/validation_reports/il/8ili | HTTPS FTP |
-Related structure data
Related structure data | 8ildC 8ileC 8ilfC 8ilgC 8ilhC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: DNA chain | Mass: 2490.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Protein | Mass: 20522.643 Da / Num. of mol.: 4 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 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: ammonium sulfate (0.2 M), Bis-Tris pH 6.5 (0.1 M), 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 19, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. obs: 69608 / % possible obs: 97.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Χ2: 0.046 / Net I/σ(I): 9.6 / Num. measured all: 346977 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.713 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 23.102 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→30 Å
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Refine LS restraints |
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