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Yorodumi- PDB-1no7: Structure of the Large Protease Resistant Upper Domain of VP5, th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1no7 | ||||||
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Title | Structure of the Large Protease Resistant Upper Domain of VP5, the Major Capsid Protein of Herpes Simplex Virus-1 | ||||||
Components | Major capsid protein | ||||||
Keywords | VIRAL PROTEIN / novel fold / alpha plus beta / viral capsid protein / folding nucleus | ||||||
Function / homology | T=16 icosahedral viral capsid / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / host cell nucleus / structural molecule activity / Major capsid protein Function and homology information | ||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Bowman, B.R. / Baker, M.L. / Rixon, F.J. / Chiu, W. / Quiocho, F.A. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Structure of the herpesvirus major capsid protein Authors: Bowman, B.R. / Baker, M.L. / Rixon, F.J. / Chiu, W. / 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 | 1no7.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1no7.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 1no7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/1no7 ftp://data.pdbj.org/pub/pdb/validation_reports/no/1no7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 65169.766 Da / Num. of mol.: 2 / Fragment: VP5 upper domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Genus: Simplexvirus / Gene: UL19 / Plasmid: pET32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06491 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.87 Å3/Da / Density % sol: 74.55 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: sodium acetate, imidazole, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.9→50 Å / Num. obs: 47194 / % possible obs: 91.2 % / Biso Wilson estimate: 31 Å2 / Net I/σ(I): 7 | |||||||||||||||
Reflection shell | Highest resolution: 2.9 Å / Mean I/σ(I) obs: 3.3 / % possible all: 80.4 | |||||||||||||||
Reflection | *PLUS Num. measured all: 308549 / Rmerge(I) obs: 0.101 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 80.4 % / Rmerge(I) obs: 0.205 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→47.09 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 408294 / 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: 37.194 Å2 / ksol: 0.291374 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→47.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.254 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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