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Yorodumi- PDB-8ua5: Crystal Structure of infected cell protein 0 (ICP0) from herpes s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ua5 | |||||||||
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Title | Crystal Structure of infected cell protein 0 (ICP0) from herpes simplex virus 1 (A636-Q776) | |||||||||
Components | RL2 | |||||||||
Keywords | PROTEIN BINDING / infected cell protein 0 (ICP0) / herpes simplex virus 1 / beta barrel / dimization | |||||||||
Function / homology | Function and homology information ligase activity / transferase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / metal ion binding Similarity search - Function | |||||||||
Biological species | Human alphaherpesvirus 1 (Herpes simplex virus type 1) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Lovell, S. / Kashipathy, M. / Battaile, K.P. / Cooper, A. / Davido, D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proteins / Year: 2024 Title: HSV-1 ICP0 dimer domain adopts a novel beta-barrel fold. Authors: McCloskey, E. / Kashipathy, M. / Cooper, A. / Gao, P. / Johnson, D.K. / Battaile, K.P. / Lovell, S. / Davido, D.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ua5.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ua5.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ua5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ua5_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 8ua5_full_validation.pdf.gz | 449.1 KB | Display | |
Data in XML | 8ua5_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 8ua5_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/8ua5 ftp://data.pdbj.org/pub/pdb/validation_reports/ua/8ua5 | HTTPS FTP |
-Related structure data
Related structure data | 8ua2C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17842.926 Da / Num. of mol.: 2 / Fragment: A636-Q776 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human alphaherpesvirus 1 (Herpes simplex virus type 1) Gene: RL2, RL2_1, HHV1gp002, HHV1gp082 / Plasmid: pTBSG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H9E965 #2: Chemical | ChemComp-CL / | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PACT G3: 20% (w/v) PEG 3350, 100 mM Bis-Tris Propane pH 7.5, 200 mM NaI, 80% crystallization solution and 20% (v/v) PEG 200. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→43.45 Å / Num. obs: 14026 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.048 / Rrim(I) all: 0.124 / Χ2: 0.72 / Net I/σ(I): 13.1 / Num. measured all: 89786 |
Reflection shell | Resolution: 2.45→2.55 Å / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.926 / Num. measured all: 9814 / Num. unique obs: 1562 / CC1/2: 0.714 / Rpim(I) all: 0.402 / Rrim(I) all: 1.012 / Χ2: 0.48 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.45 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.29 / 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: 2.45→43.45 Å
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Refine LS restraints |
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LS refinement shell |
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