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Yorodumi- PDB-4lif: Crystal structure of the JCV large T-antigen origin binding domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lif | ||||||
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Title | Crystal structure of the JCV large T-antigen origin binding domain | ||||||
Components | Large T antigenLarge tumor antigen | ||||||
Keywords | Hydrolase / dna binding protein / origin binding domain / replication / polyomavirus | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | JC polyomavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Meinke, G. / Bohm, A. / Bullock, P. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lif.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lif.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 4lif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/4lif ftp://data.pdbj.org/pub/pdb/validation_reports/li/4lif | HTTPS FTP |
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-Related structure data
Related structure data | 4lmdC 4nbpC 2fufS C: citing same article (ref.) S: Starting model for refinement |
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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: 15170.390 Da / Num. of mol.: 1 / Fragment: OBD (unp residues 132-261) Source method: isolated from a genetically manipulated source Source: (gene. exp.) JC polyomavirus / Gene: Large T antigen / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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