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- PDB-7rr3: Structure of Deep-Sea Phage NrS-1 Primase-Polymerase N300 in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rr3 | ||||||
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Title | Structure of Deep-Sea Phage NrS-1 Primase-Polymerase N300 in complex with calcium and ddCTP | ||||||
![]() | Primase | ||||||
![]() | REPLICATION / primpol / denovo / polymerase | ||||||
Function / homology | ![]() viral DNA genome replication / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA replication / DNA helicase / DNA-directed DNA polymerase / hydrolase activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, L. / Yu, C. / Sliz, P. | ||||||
Funding support | 1items
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![]() | ![]() Title: Molecular Dissection of the Primase and Polymerase Activities of Deep-Sea Phage NrS-1 Primase-Polymerase. Authors: Huang, F. / Lu, X. / Yu, C. / Sliz, P. / Wang, L. / Zhu, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.8 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 687.4 KB | Display | ![]() |
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Full document | ![]() | 688.7 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 33169.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DCT / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% (w/v) PEG 3000, 200 mM calcium acetate, and 100 mM Tris-HCl (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→51.1 Å / Num. obs: 26214 / % possible obs: 97.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.1572 / Net I/σ(I): 11.39 |
Reflection shell | Resolution: 2.24→2.32 Å / Rmerge(I) obs: 1.35 / Num. unique obs: 1419 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 51.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→51.1 Å
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Refine LS restraints |
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LS refinement shell |
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