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- PDB-5n2g: Structure of the E9 DNA polymerase from vaccinia virus in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n2g | ||||||
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Title | Structure of the E9 DNA polymerase from vaccinia virus in complex with manganese | ||||||
![]() | DNA polymerase | ||||||
![]() | TRANSFERASE / Vaccinia virus / DNA polymerase / protein-protein interface / family B polymerase / processivity factor | ||||||
Function / homology | ![]() viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tarbouriech, N. / Burmeister, W.P. / Iseni, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. Authors: Tarbouriech, N. / Ducournau, C. / Hutin, S. / Mas, P.J. / Man, P. / Forest, E. / Hart, D.J. / Peyrefitte, C.N. / Burmeister, W.P. / Iseni, F. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227 KB | Display | ![]() |
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PDB format | ![]() | 176.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.8 KB | Display | ![]() |
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Full document | ![]() | 492.9 KB | Display | |
Data in XML | ![]() | 37.9 KB | Display | |
Data in CIF | ![]() | 54.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n2eSC ![]() 5n2hC 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 117316.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P20509, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters |
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-Non-polymers , 6 types, 226 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | #5: Chemical | ChemComp-DTT / | #6: Chemical | ChemComp-EPE / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 9-11% PEG 3000, 20-25% glycerol, 100 mM MES-NaOH pH 6.25, 5 mM MnCl2 PH range: 6.0-6.5 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0714 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→46 Å / Num. obs: 59597 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rrim(I) all: 0.108 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.79→2.89 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 5772 / Rrim(I) all: 0.958 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N2E Resolution: 2.78→46 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.218 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.25 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.326 Å2
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Refinement step | Cycle: 1 / Resolution: 2.78→46 Å
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Refine LS restraints |
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