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- PDB-4r94: Structure of the nickase domain of NS1 from MVM complexed with ma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r94 | ||||||
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Title | Structure of the nickase domain of NS1 from MVM complexed with magnesium | ||||||
![]() | Non-structural protein NS1 | ||||||
![]() | REPLICATION / nickase domain / DNA binding / magnesium / nickase | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Liang, L. / 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 | ![]() | 71.2 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.7 KB | Display | ![]() |
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Full document | ![]() | 423.7 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wrnC ![]() 3wroC ![]() 3wrqC ![]() 3wrrC ![]() 3wrsC ![]() 4pp4SC 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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Unit cell |
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Components
#1: Protein | Mass: 30040.857 Da / Num. of mol.: 1 / Fragment: nickase domain (UNP RESIDUES 1-255) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.64 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2014 Details: K-B pair of biomorph mirrors with two additional horizontally deflecting mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.668→50 Å / Num. obs: 34417 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 37.118 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3.125 / Rsym value: 0.453 / % possible all: 95.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4PP4 Resolution: 1.668→19.676 Å / SU ML: 0.15 / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 1.35 / Phase error: 21.03 / Stereochemistry target values: ML
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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: 29.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.668→19.676 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: 12
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