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Yorodumi- PDB-2itj: Origin binding domain of the SV40 large T antigen (residues 131-2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2itj | ||||||
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Title | Origin binding domain of the SV40 large T antigen (residues 131-259). P212121 crystal form | ||||||
Components | large T antigenLarge tumor antigen | ||||||
Keywords | DNA BINDING PROTEIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Martynowski, D. / Bochkareva, E. / 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 | 2itj.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2itj.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 2itj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/2itj ftp://data.pdbj.org/pub/pdb/validation_reports/it/2itj | HTTPS FTP |
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-Related structure data
Related structure data | 2iprSC 2itlC 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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-Components
#1: 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 #2: 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: 2 Å3/Da / Density % sol: 38.35 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 mM NaAc, 20% PEG4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 29, 2002 / Details: mirirs |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 8118 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rsym value: 0.088 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique all: 751 / Rsym value: 0.435 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IPR Resolution: 2.5→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å |