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Yorodumi- PDB-2f5u: Structural Characterization of the UL25 DNA Packaging Protein fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f5u | ||||||
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Title | Structural Characterization of the UL25 DNA Packaging Protein from Herpes Simplex Virus Type 1 | ||||||
Components | Virion protein UL25Virus | ||||||
Keywords | VIRAL PROTEIN / HSV-1 / Capsid Protein / DNA packaging / UL25 / Head Completion | ||||||
Function / homology | Herpesvirus UL25 / Herpesvirus UL25 family / viral genome packaging / viral release from host cell / viral penetration into host nucleus / viral capsid / symbiont entry into host cell / host cell nucleus / Capsid vertex component 2 Function and homology information | ||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Bowman, B.R. | ||||||
Citation | Journal: J.Virol. / Year: 2006 Title: Structural characterization of the UL25 DNA-packaging protein from herpes simplex virus type 1 Authors: Bowman, B.R. / Welschhans, R.L. / Jayaram, H. / Stow, N.D. / Preston, V.G. / Quiocho, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f5u.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f5u.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 2f5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/2f5u ftp://data.pdbj.org/pub/pdb/validation_reports/f5/2f5u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | possible monomer |
-Components
#1: Protein | Mass: 48433.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Genus: Simplexvirus / Gene: UL25 / Production host: Escherichia coli (E. coli) / References: UniProt: P10209 |
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#2: 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: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15-25% PEG MME 2000, 200mM Triethylamine N-oxide hydrate, 100mM Tris pH 8.0 to 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: .97948, .97937 | |||||||||
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Detector | Type: SBC-2 / Detector: CCD / Date: Jun 24, 2004 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. all: 191657 / Num. obs: 191657 / % possible obs: 97.9 % / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 14.1 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→34.1 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1958343.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.3781 Å2 / ksol: 0.344785 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→34.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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