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- PDB-7pbk: Vibriophage phiVC8 family A DNA polymerase (DpoZ), two conformati... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pbk | ||||||
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Title | Vibriophage phiVC8 family A DNA polymerase (DpoZ), two conformations: thumb-exo open and thumb-exo closed | ||||||
![]() | DNA polymerase I![]() | ||||||
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Function / homology | ![]() viral DNA genome replication / 3'-5' exonuclease activity / DNA-templated DNA replication / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Czernecki, D. / Hu, H. / Romoli, F. / Delarue, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage phi VC8. Authors: Czernecki, D. / Hu, H. / Romoli, F. / Delarue, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 528.6 KB | Display | ![]() |
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PDB format | ![]() | 379.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ktqS S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 72842.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow![]() | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 300 mM ammonium citrate; 12% PEG 3350. Seeded from crystals grown at 291.15 K in 1 mM hexamine cobalt; 25% v/v isopropanol (100%); 100 mM HEPES pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2016 / Details: KB mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.79→48.35 Å / Num. obs: 1019252 / % possible obs: 99.4 % / Redundancy: 26.5 % / Biso Wilson estimate: 61.06 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.352 / Rpim(I) all: 0.069 / Rrim(I) all: 0.359 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.79→2.87 Å / Redundancy: 23.5 % / Rmerge(I) obs: 2.617 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2621 / CC1/2: 0.413 / Rpim(I) all: 0.529 / Rrim(I) all: 2.673 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1KTQ Resolution: 2.8→48.35 Å / SU ML: 0.3986 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.892 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 56.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 46.777303748 Å / Origin y: 176.763914675 Å / Origin z: 23.5622800401 Å
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Refinement TLS group | Selection details: all |