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- PDB-4lif: Crystal structure of the JCV large T-antigen origin binding domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lif | ||||||
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Title | Crystal structure of the JCV large T-antigen origin binding domain | ||||||
![]() | Large T antigen | ||||||
![]() | Hydrolase / dna binding protein / origin binding domain / replication / polyomavirus | ||||||
Function / homology | ![]() symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / DNA replication / symbiont-mediated suppression of host innate immune response / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell nucleus ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / DNA replication / symbiont-mediated suppression of host innate immune response / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell nucleus / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meinke, G. / Bohm, A. / Bullock, P. | ||||||
![]() | ![]() Title: Insights into the Initiation of JC Virus DNA Replication Derived from the Crystal Structure of the T-Antigen Origin Binding Domain. Authors: Meinke, G. / Phelan, P.J. / Kalekar, R. / Shin, J. / Archambault, J. / Bohm, A. / Bullock, P.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.4 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4lmdC ![]() 4nbpC ![]() 2fufS C: citing same article ( S: Starting model for refinement |
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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: 15170.390 Da / Num. of mol.: 1 / Fragment: OBD (unp residues 132-261) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P03072, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.25 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris, 0.2 M LiSO4, 30 % Peg 4000, VAPOR DIFFUSION, SITTING DROP, temperature 273K, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 5909 / Num. obs: 5906 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 72.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 37.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2FUF Resolution: 2.6→36.696 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.39 / Phase error: 25.57 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→36.696 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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