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- PDB-5m1o: Crystal structure of the large terminase nuclease from thermophil... -

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Basic information

Entry
Database: PDB / ID: 5m1o
TitleCrystal structure of the large terminase nuclease from thermophilic phage G20c with bound Cobalt
ComponentsPhage terminase large subunit
KeywordsVIRAL PROTEIN / large terminase / nuclease domain / Hydrolase
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 G20c (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsXu, R.G. / Jenkins, H.T. / Chechik, M. / Blagova, E.V. / Greive, S.J. / Antson, A.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
Wellcome Trust101528 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism.
Authors: Xu, R.G. / Jenkins, H.T. / Chechik, M. / Blagova, E.V. / Lopatina, A. / Klimuk, E. / Minakhin, L. / Severinov, K. / Greive, S.J. / Antson, A.A.
History
DepositionOct 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage terminase large subunit
B: Phage terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4674
Polymers42,3502
Non-polymers1182
Water5,747319
1
A: Phage terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2342
Polymers21,1751
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phage terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2342
Polymers21,1751
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.937, 53.895, 69.751
Angle α, β, γ (deg.)90.000, 91.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phage terminase large subunit


Mass: 21174.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage G20c (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4BKS3*PLUS
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Tartrate, 0.1 M Bis-tris pH 5.5-6.5, 20% PEG 3350
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.6→42.92 Å / Num. obs: 40243 / % possible obs: 95.7 % / Redundancy: 2.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.057 / Rrim(I) all: 0.092 / Net I/σ(I): 6.6 / Num. measured all: 86303
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.6-1.6320.7250.604189.5
8.76-42.922.20.0280.998190.1

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.92 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.934 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2038 5.1 %RANDOM
Rwork0.1849 ---
obs0.1868 38195 95.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.05 Å2 / Biso mean: 22.409 Å2 / Biso min: 11.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å2-0.82 Å2
2---1.03 Å2-0 Å2
3----0.91 Å2
Refinement stepCycle: final / Resolution: 1.6→42.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 2 322 3238
Biso mean--26.97 30.99 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193042
X-RAY DIFFRACTIONr_bond_other_d0.0020.022832
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9584138
X-RAY DIFFRACTIONr_angle_other_deg0.88336484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90823.793145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03715494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5731524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023553
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02719
X-RAY DIFFRACTIONr_mcbond_it1.0832.1221541
X-RAY DIFFRACTIONr_mcbond_other1.0812.1211540
X-RAY DIFFRACTIONr_mcangle_it1.8183.171935
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 128 -
Rwork0.321 2688 -
all-2816 -
obs--91.28 %

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