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Yorodumi- PDB-5vyl: Crystal Structure of N-terminal half of Herpes Simplex virus Type... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vyl | ||||||||||||
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Title | Crystal Structure of N-terminal half of Herpes Simplex virus Type 1 UL37 protein | ||||||||||||
Components | Inner tegument protein | ||||||||||||
Keywords | VIRAL PROTEIN | ||||||||||||
Function / homology | Function and homology information microtubule-dependent intracellular transport of viral material towards cell periphery / protein-glutamine glutaminase activity / protein-glutamine glutaminase / viral tegument / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / virion assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell Golgi apparatus / host cell nucleus / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å | ||||||||||||
Authors | Koenigsberg, A. / Heldwein, E.E. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J. Virol. / Year: 2017 Title: Crystal Structure of the N-Terminal Half of the Traffic Controller UL37 from Herpes Simplex Virus 1. Authors: Koenigsberg, A.L. / Heldwein, E.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vyl.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vyl.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vyl_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 5vyl_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 5vyl_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5vyl_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/5vyl ftp://data.pdbj.org/pub/pdb/validation_reports/vy/5vyl | HTTPS FTP |
-Related structure data
Related structure data | 4k70S 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: 61799.551 Da / Num. of mol.: 1 / Fragment: residues 1-575 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Strain: 17 / Gene: UL37 / Plasmid: pET24 Details (production host): N-terminal His-SUMO tag cleavable by HRV3C protease Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LOBSTR / References: UniProt: P10221 |
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#2: Chemical | ChemComp-NA / |
#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: 3.66 Å3/Da / Density % sol: 66.43 % / Description: Needles |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M Bicine pH 9.0, 8% PEG 20K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.51→164.22 Å / Num. obs: 12161 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 97.01 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.441 / Rpim(I) all: 0.119 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.51→3.85 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.993 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2818 / CC1/2: 0.58 / Rpim(I) all: 0.539 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4k70 Resolution: 3.51→96.737 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.51→96.737 Å
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Refine LS restraints |
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LS refinement shell |
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