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- PDB-5m1k: Crystal structure of the large terminase nuclease from thermophil... -

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Basic information

Entry
Database: PDB / ID: 5m1k
TitleCrystal structure of the large terminase nuclease from thermophilic phage G20c with bound Magnesium
ComponentsPhage terminase large subunit
KeywordsVIRAL PROTEIN / large terminase / nuclease domain
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: 1.2 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)42,7756
Polymers42,3502
Non-polymers4264
Water8,305461
1
A: Phage terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2712
Polymers21,1751
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phage terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5044
Polymers21,1751
Non-polymers3303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.807, 54.057, 69.950
Angle α, β, γ (deg.)90.000, 91.940, 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
Details: scientific_name: 'Thermus phage G20c' ncbi_taxonomy_id: 1406341 The same as entry.id 4XVN
Source: (gene. exp.) Thermus phage G20c (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4BKS3*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 1.97 Å3/Da / Density % sol: 37.41 %
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: 1.2→43.78 Å / Num. obs: 98722 / % possible obs: 97 % / Redundancy: 2.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.054 / Rrim(I) all: 0.091 / Net I/σ(I): 7.4 / Num. measured all: 250958
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.2-1.222.50.7650.522197.6
6.57-43.782.70.0430.991194

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimlessdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→43.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.934 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 4820 4.9 %RANDOM
Rwork0.1832 ---
obs0.1845 93879 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 44.99 Å2 / Biso mean: 14.409 Å2 / Biso min: 6.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.11 Å2
2--0.51 Å20 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 1.2→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 30 470 3428
Biso mean--17.22 26.88 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193134
X-RAY DIFFRACTIONr_bond_other_d0.0010.022889
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9654274
X-RAY DIFFRACTIONr_angle_other_deg0.8836631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.785406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56524.11146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16915508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5741522
X-RAY DIFFRACTIONr_chiral_restr0.0780.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023678
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02732
X-RAY DIFFRACTIONr_mcbond_it0.7961.261585
X-RAY DIFFRACTIONr_mcbond_other0.7851.2591584
X-RAY DIFFRACTIONr_mcangle_it1.3221.8882004
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 394 -
Rwork0.309 6911 -
all-7305 -
obs--97.36 %

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