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Yorodumi- PDB-1svm: Co-crystal structure of SV40 large T antigen helicase domain and ATP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1svm | ||||||
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Title | Co-crystal structure of SV40 large T antigen helicase domain and ATP | ||||||
Components | large T antigenLarge tumor antigen | ||||||
Keywords | VIRAL PROTEIN / AAA+ fold | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / double-stranded DNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Simian virus 40 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Gai, D. / Zhao, R. / Finkielstein, C.V. / Chen, X.S. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2004 Title: Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Authors: Gai, D. / Zhao, R. / Li, D. / Finkielstein, C.V. / Chen, X.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1svm.cif.gz | 456.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1svm.ent.gz | 374.5 KB | Display | PDB format |
PDBx/mmJSON format | 1svm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/1svm ftp://data.pdbj.org/pub/pdb/validation_reports/sv/1svm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43541.422 Da / Num. of mol.: 6 / Fragment: HELICASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / Production host: Escherichia coli (E. coli) / References: UniProt: P03070 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ATP / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.25 Details: Tris, magnesium chloride, PEG 8000, DTT, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Detector: CCD |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→30 Å / Num. all: 241728 / Num. obs: 223206 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.94→1.97 Å / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→30 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.94→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.95 Å
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