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- PDB-3wrq: Minute virus of mice non-structural protein-1N-terminal nuclease ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wrq | ||||||
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Title | Minute virus of mice non-structural protein-1N-terminal nuclease domain reveals a unique Zn2+ coordination in the active site pocket and shows a novel mode of DNA recognition at the origin of replication | ||||||
![]() | Non-capsid protein NS-1 | ||||||
![]() | REPLICATION / Nuclease activity / Single and double stranded DNA binding / nicking protein | ||||||
Function / homology | ![]() rolling hairpin viral DNA replication / symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host transcription / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / endonuclease activity / DNA helicase / DNA replication / host cell nucleus ...rolling hairpin viral DNA replication / symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host transcription / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / endonuclease activity / DNA helicase / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tewary, S.K. / Zhao, H. / Tang, L. | ||||||
![]() | ![]() Title: Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding. Authors: Tewary, S.K. / Liang, L. / Lin, Z. / Lynn, A. / Cotmore, S.F. / Tattersall, P. / Zhao, H. / Tang, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.6 KB | Display | ![]() |
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PDB format | ![]() | 94 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.2 KB | Display | ![]() |
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Full document | ![]() | 426.8 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wrnC ![]() 3wroC ![]() 3wrrC ![]() 3wrsC ![]() 4pp4C ![]() 4r94C 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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Unit cell |
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Components
#1: Protein | Mass: 32343.402 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 2.8M sodium formate, 100mM sodium acetate trihydrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2014 / Details: Mirrors-Rh coated |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.53 Å / Num. obs: 43991 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→30.315 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Origin x: 4.869 Å / Origin y: 42.7319 Å / Origin z: 20.7703 Å
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Refinement TLS group | Selection details: CHAIN A |