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- PDB-4iox: The structure of the herpes simplex virus DNA-packaging motor pUL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iox | ||||||
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Title | The structure of the herpes simplex virus DNA-packaging motor pUL15 C-terminal nuclease domain provides insights into cleavage of concatemeric viral genome precursors | ||||||
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![]() | VIRAL PROTEIN / nuclease | ||||||
Function / homology | ![]() chromosome organization / Hydrolases; Acting on ester bonds / hydrolase activity / host cell nucleus / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Selvarajan Sigamani, S. / Zhao, H. / Kamau, Y. / Tang, L. | ||||||
![]() | ![]() Title: The Structure of the Herpes Simplex Virus DNA-Packaging Terminase pUL15 Nuclease Domain Suggests an Evolutionary Lineage among Eukaryotic and Prokaryotic Viruses. Authors: Selvarajan Sigamani, S. / Zhao, H. / Kamau, Y.N. / Baines, J.D. / Tang, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268 KB | Display | ![]() |
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PDB format | ![]() | 218.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.3 KB | Display | ![]() |
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Full document | ![]() | 504.3 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n4pS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 30918.906 Da / Num. of mol.: 3 / Fragment: C-terminal domain (UNP residues 471-735) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: UL15 / Plasmid: pET28b / Production host: ![]() ![]() #2: Protein/peptide | | Mass: 528.644 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET28b / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 50 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PGE / |
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#4: Chemical | ChemComp-PEG / |
#5: Chemical | ChemComp-PG4 / |
#6: Chemical | ChemComp-ACT / |
#7: Water | ChemComp-HOH / |
-Details
Sequence details | CHAIN D MAY CORRESPOND |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1 M ammonium citrate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2012 / Details: Rh coated flat mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.458→50 Å / Num. all: 34540 / Num. obs: 34365 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 42.92 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3N4P Resolution: 2.458→19.799 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 26.48 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.458→19.799 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 56.6268 Å / Origin y: 36.7358 Å / Origin z: 11.8879 Å
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Refinement TLS group | Selection details: all |