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- PDB-4znk: Thermus Phage P74-26 Large Terminase ATPase domain from (P 32 2 1... -

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Basic information

Entry
Database: PDB / ID: 4znk
TitleThermus Phage P74-26 Large Terminase ATPase domain from (P 32 2 1 space group)
ComponentsPhage terminase large subunit
KeywordsVIRAL PROTEIN / DNA Translocation
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
Terminase, large subunit, gp17-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Terminase, large subunit
Similarity search - Component
Biological speciesThermus phage P7426 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.931 Å
AuthorsHilbert, B.J. / Hayes, J.A. / Stone, N.P. / Duffy, C.M. / Kelch, B.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Hudson Hoagland Society United States
Pew Charitable Trusts United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure and mechanism of the ATPase that powers viral genome packaging.
Authors: Hilbert, B.J. / Hayes, J.A. / Stone, N.P. / Duffy, C.M. / Sankaran, B. / Kelch, B.A.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9655
Polymers31,5811
Non-polymers3844
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.890, 62.890, 133.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

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Components

#1: Protein Phage terminase large subunit


Mass: 31580.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage P7426 (virus) / Gene: P74p84 / Plasmid: pet24a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR DE3 / References: UniProt: A7XXR1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 11% (w/v) PEG 2000, 0.15 M ammonium sulfate, and 0.1 M tri-sodium citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.931→34.4 Å / Num. obs: 23556 / % possible obs: 99.68 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.71
Reflection shellResolution: 1.931→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.96 / % possible all: 97.75

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZNI
Resolution: 1.931→34.398 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1965 1173 4.98 %
Rwork0.1508 --
obs0.153 23550 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.931→34.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 20 209 2333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092204
X-RAY DIFFRACTIONf_angle_d1.1732993
X-RAY DIFFRACTIONf_dihedral_angle_d13.465809
X-RAY DIFFRACTIONf_chiral_restr0.048303
X-RAY DIFFRACTIONf_plane_restr0.005389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.931-2.01850.26171400.21032714X-RAY DIFFRACTION98
2.0185-2.12490.24951480.17952745X-RAY DIFFRACTION100
2.1249-2.25810.21181440.15492764X-RAY DIFFRACTION100
2.2581-2.43240.20781460.14322766X-RAY DIFFRACTION100
2.4324-2.67710.19741440.14812769X-RAY DIFFRACTION100
2.6771-3.06420.21471510.1422808X-RAY DIFFRACTION100
3.0642-3.85980.15541510.13942835X-RAY DIFFRACTION100
3.8598-34.40360.18891490.1492976X-RAY DIFFRACTION100

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