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- PDB-5tge: Thermus Phage P74-26 Large Terminase Nuclease Domain -

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Basic information

Entry
Database: PDB / ID: 5tge
TitleThermus Phage P74-26 Large Terminase Nuclease Domain
ComponentsPhage terminase large subunit
KeywordsVIRAL PROTEIN / nuclease
Function / homology
Function and homology information


viral terminase, large subunit / viral DNA genome packaging / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Nucleotidyltransferase; domain 5 - #240 / Terminase, large subunit, gp17-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / Nucleotidyltransferase; domain 5 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Terminase, large subunit
Similarity search - Component
Biological speciesThermus phage P7426 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsHilbert, B.J. / Hayes, J.A. / Stone, N.P. / Kelch, B.A.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain.
Authors: Hilbert, B.J. / Hayes, J.A. / Stone, N.P. / Xu, R.G. / Kelch, B.A.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage terminase large subunit


Theoretical massNumber of molelcules
Total (without water)27,8491
Polymers27,8491
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.370, 71.370, 127.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phage terminase large subunit


Mass: 27849.109 Da / Num. of mol.: 1 / Fragment: residues 257-485
Source method: isolated from a genetically manipulated source
Details: synthetic construct / Source: (gene. exp.) Thermus phage P7426 (virus) / Gene: P74p84 / Plasmid: pET28
Details (production host): Thrombin site replaced by prescission protease site
Production host: Escherichia coli (E. coli) / Strain (production host): BLR-DE3 / References: UniProt: A7XXR1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20 mg/mL protein mixed 2:1 with buffer containing 0.23M sodium phosphate monobasic/potassium phosphate dibasic pH 6.2 and 2.5M sodium chloride, and 4 mM dTMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 10480 / % possible obs: 98 % / Redundancy: 28 % / CC1/2: 0.999 / Rsym value: 0.089 / Net I/σ(I): 23.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX(1.10_2155)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→47.507 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 23.72
RfactorNum. reflection% reflection
Rfree0.2454 524 5 %
Rwork0.2198 --
obs0.2211 10478 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 0 99 1601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031530
X-RAY DIFFRACTIONf_angle_d0.5042071
X-RAY DIFFRACTIONf_dihedral_angle_d11.145912
X-RAY DIFFRACTIONf_chiral_restr0.041227
X-RAY DIFFRACTIONf_plane_restr0.002269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.86180.31471220.26172321X-RAY DIFFRACTION93
2.8618-3.27580.27041310.23762474X-RAY DIFFRACTION100
3.2758-4.12680.24261300.20792480X-RAY DIFFRACTION99
4.1268-47.51520.21471410.20592679X-RAY DIFFRACTION100

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