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- PDB-4iox: The structure of the herpes simplex virus DNA-packaging motor pUL... -

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Basic information

Entry
Database: PDB / ID: 4iox
TitleThe structure of the herpes simplex virus DNA-packaging motor pUL15 C-terminal nuclease domain provides insights into cleavage of concatemeric viral genome precursors
Components
  • Tripartite terminase subunit UL15
  • peptide
KeywordsVIRAL PROTEIN / nuclease
Function / homology
Function and homology information


chromosome organization / Hydrolases; Acting on ester bonds / hydrolase activity / host cell nucleus / DNA binding
Similarity search - Function
DNA-packaging terminase, C-terminal nuclease domain / Probable DNA packing protein, C-terminal / Probable DNA packing protein, N-terminal / Tripartite terminase subunit 3 / Probable DNA packing protein, C-terminal domain superfamily / Probable DNA packing protein, C-terminus / Probable DNA packing protein, N-terminus / Nucleotidyltransferase; domain 5 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Tripartite terminase subunit 3
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.458 Å
AuthorsSelvarajan Sigamani, S. / Zhao, H. / Kamau, Y. / Tang, L.
CitationJournal: J.Virol. / Year: 2013
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
DepositionJan 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tripartite terminase subunit UL15
B: Tripartite terminase subunit UL15
C: Tripartite terminase subunit UL15
D: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7958
Polymers93,2854
Non-polymers5104
Water82946
1
A: Tripartite terminase subunit UL15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4285
Polymers30,9191
Non-polymers5104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tripartite terminase subunit UL15


Theoretical massNumber of molelcules
Total (without water)30,9191
Polymers30,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tripartite terminase subunit UL15


Theoretical massNumber of molelcules
Total (without water)30,9191
Polymers30,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: peptide


  • defined by author&software
  • 529 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5291
Polymers5291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.944, 96.944, 194.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Tripartite terminase subunit UL15 / DNA-packaging protein UL15 / Terminase large subunit


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.) Human herpesvirus 1 (Herpes simplex virus type 1)
Gene: UL15 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P04295
#2: Protein/peptide peptide


Mass: 528.644 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)

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Non-polymers , 5 types, 50 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAIN D MAY CORRESPOND TO A SUBSET OF UNOBSERVED CHAIN C RESIDUES 689-704.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2012 / Details: Rh coated flat mirror
RadiationMonochromator: 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 wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 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
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.458-2.59.10.482.616351100
2.5-2.559.80.473.21640198.1
2.55-2.610.70.4241662199.4
2.6-2.6512.30.365.71709199.9
2.65-2.7112.70.346.917091100
2.71-2.7713.20.288.416781100
2.77-2.8413.20.2510.117111100
2.84-2.9213.10.2212.216891100
2.92-312.90.1914.517121100
3-3.112.30.1618.417031100
3.1-3.2112.10.1421.617191100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N4P

3n4p


Resolution: 2.458→19.799 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1718 5.01 %RANDOM
Rwork0.2028 ---
obs0.205 34293 99.54 %-
all-34593 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.77 Å2
Refinement stepCycle: LAST / Resolution: 2.458→19.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 34 46 5172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015243
X-RAY DIFFRACTIONf_angle_d1.357126
X-RAY DIFFRACTIONf_dihedral_angle_d16.9121853
X-RAY DIFFRACTIONf_chiral_restr0.092826
X-RAY DIFFRACTIONf_plane_restr0.008913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.458-2.52980.30661350.25762560X-RAY DIFFRACTION95
2.5298-2.61130.31361400.23062660X-RAY DIFFRACTION99
2.6113-2.70440.2551410.21792670X-RAY DIFFRACTION100
2.7044-2.81240.26981410.22272677X-RAY DIFFRACTION100
2.8124-2.940.27511430.22982706X-RAY DIFFRACTION100
2.94-3.09440.31511410.23482675X-RAY DIFFRACTION100
3.0944-3.28750.30091410.23642703X-RAY DIFFRACTION100
3.2875-3.540.27061440.2052703X-RAY DIFFRACTION100
3.54-3.89380.25261450.18872751X-RAY DIFFRACTION100
3.8938-4.45170.20261430.16752737X-RAY DIFFRACTION100
4.4517-5.58760.23141480.182795X-RAY DIFFRACTION100
5.5876-19.79920.21711560.21472938X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 56.6268 Å / Origin y: 36.7358 Å / Origin z: 11.8879 Å
111213212223313233
T0.3639 Å2-0.0166 Å2-0.0491 Å2-0.297 Å20.0416 Å2--0.4978 Å2
L0.5702 °2-0.1437 °2-0.056 °2-0.4471 °20.253 °2--0.5053 °2
S0.0107 Å °-0.0214 Å °-0.1035 Å °0.1706 Å °0.0011 Å °-0.0697 Å °0.1718 Å °0.0138 Å °-0.0079 Å °
Refinement TLS groupSelection details: all

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