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Yorodumi- PDB-4fgn: Crystal structure of the SV40 large T-antigen origin bining domai... -
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-Basic information
Entry | Database: PDB / ID: 4fgn | ||||||
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Title | Crystal structure of the SV40 large T-antigen origin bining domain bound to Site I DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / origin binding domain / 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 / 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: 3.2 Å | ||||||
Authors | Meinke, G. / Bohm, A. / Bullock, P.A. | ||||||
Citation | Journal: J.Virol. / Year: 2013 Title: Analysis of the Costructure of the Simian Virus 40 T-Antigen Origin Binding Domain with Site I Reveals a Correlation between GAGGC Spacing and Spiral Assembly. Authors: Meinke, G. / Phelan, P.J. / Harrison, C.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 | 4fgn.cif.gz | 170.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fgn.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/4fgn ftp://data.pdbj.org/pub/pdb/validation_reports/fg/4fgn | HTTPS FTP |
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-Related structure data
Related structure data | 2ntcS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15240.476 Da / Num. of mol.: 2 / Fragment: origin binding domain, UNP residues 131-260 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian virus 40 / 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 #2: DNA chain | | Mass: 6963.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This DNA sequence is termed Site 1 in SV40 / Source: (synth.) Simian virus 40 #3: DNA chain | | Mass: 7158.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This DNA sequence is from sv40 site I / Source: (synth.) Simian virus 40 #4: 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: 3.03 Å3/Da / Density % sol: 59.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M sodium acetate pH 4.6, .2M ammonium sulfate, 30 % Peg 4000, 10 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 9304 / % possible obs: 100 % / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 3.2→3.31 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NTC Resolution: 3.2→47.99 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 73.091 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 137.11 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→47.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.28 Å / Total num. of bins used: 20
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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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