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Yorodumi- PDB-2itl: The origin binding domain of the SV40 large T antigen bound to th... -
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-Basic information
Entry | Database: PDB / ID: 2itl | ||||||
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Title | The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp) | ||||||
Components |
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Keywords | DNA binding protein/DNA / DNA binding protein / DNA binding protein-DNA COMPLEX | ||||||
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 / DNA replication / 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: 1.65 Å | ||||||
Authors | Bochkareva, E. / Seitova, A. / Bochkarev, A. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA Authors: Bochkareva, E. / Martynowski, D. / Seitova, A. / Bochkarev, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2itl.cif.gz | 172.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2itl.ent.gz | 132.5 KB | Display | PDB format |
PDBx/mmJSON format | 2itl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/2itl ftp://data.pdbj.org/pub/pdb/validation_reports/it/2itl | HTTPS FTP |
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-Related structure data
Related structure data | 2iprSC 2itjC 2nl8C 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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Details | The biological assembly is a dsDNA fragment bound by four OBDs |
-Components
#1: DNA chain | Mass: 7397.742 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 7357.718 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 15380.704 Da / Num. of mol.: 2 / Fragment: Origin binding domain (residues 131-259) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / Strain: 776 / Gene: large T antigen / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P03070, UniProt: Q98ZP7*PLUS #4: 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: 1.96 Å3/Da / Density % sol: 37.35 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 mM di-ammonium hydrogen citrate, 20% PEG 3000, and 10 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9176 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9176 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. all: 42961 / Num. obs: 42961 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.062 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.65→1.71 Å / Num. unique all: 4204 / Rsym value: 0.213 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IPR Resolution: 1.65→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.384 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.282 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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