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Yorodumi- PDB-3qk2: Structure-Based Analysis of the Interaction between the Simian Vi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qk2 | ||||||
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Title | Structure-Based Analysis of the Interaction between the Simian Virus 40 T-Antigen Origin Binding Domain and Single-Stranded DNA | ||||||
Components | Large T antigen | ||||||
Keywords | DNA BINDING PROTEIN / origin binding domain / DNA replication | ||||||
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 3'-5' helicase / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / helicase activity / double-stranded DNA binding / single-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 3'-5' helicase / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / helicase activity / double-stranded DNA binding / single-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / hydrolase activity / virus-mediated perturbation of host defense response / 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: 1.643 Å | ||||||
Authors | Meinke, G. / Bullock, P.A. / Bohm, A. | ||||||
Citation | Journal: J.Virol. / Year: 2011 Title: Structure-based analysis of the interaction between the simian virus 40 T-antigen origin binding domain and single-stranded DNA. Authors: Meinke, G. / Phelan, P.J. / Fradet-Turcotte, A. / Bohm, A. / Archambault, J. / Bullock, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qk2.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qk2.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qk2_validation.pdf.gz | 430.6 KB | Display | wwPDB validaton report |
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Full document | 3qk2_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 3qk2_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 3qk2_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/3qk2 ftp://data.pdbj.org/pub/pdb/validation_reports/qk/3qk2 | HTTPS FTP |
-Related structure data
Related structure data | 5d9iC 2fufS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 15490.752 Da / Num. of mol.: 1 / Fragment: origin binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian virus 40 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) References: UniProt: P03070, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#2: Chemical | ChemComp-SCN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.73 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion Details: 0.2 M thiocyanate [SCN], 17.5% PEG 3350, 5% glycerol, VAPOR DIFFUSION, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. all: 15789 / Num. obs: 15764 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 29.38 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.46 / Num. unique all: 14985 / Rsym value: 0.474 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FUF Resolution: 1.643→44.807 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / 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 / Bsol: 45.301 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.643→44.807 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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