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- PDB-8qky: Bacteriophage T5 dUTPase -

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Basic information

Entry
Database: PDB / ID: 8qky
TitleBacteriophage T5 dUTPase
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / bacteriophage / T5 / dUTPase / Deoxyuridine triphosphate nucleotidohydrolases / dUTP
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesEscherichia phage T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGabdulkhakov, A.G. / Dzhus, U.F. / Selikhanov, G.K. / Glukhov, A.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-24-00510 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2024
Title: Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions.
Authors: Glukhov, A. / Marchenkov, V. / Dzhus, U. / Krutilina, A. / Selikhanov, G. / Gabdulkhakov, A.
History
DepositionSep 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7634
Polymers48,6713
Non-polymers921
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-69 kcal/mol
Surface area16890 Å2
Unit cell
Length a, b, c (Å)78.430, 78.430, 86.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase


Mass: 16223.650 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: DUT / Production host: Escherichia coli (E. coli) / References: UniProt: O48500
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.075 M TRIS hydrochloride, 1.5 M Ammonium sulfate, 25% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 35488 / % possible obs: 99.9 % / Redundancy: 12.76 % / Biso Wilson estimate: 35.18 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.91
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 2637 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.76 Å / SU ML: 0.221 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.5113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2109 1775 5 %
Rwork0.1776 33701 -
obs0.1793 35476 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.21 Å2
Refinement stepCycle: LAST / Resolution: 2→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 6 163 3346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663281
X-RAY DIFFRACTIONf_angle_d0.84264437
X-RAY DIFFRACTIONf_chiral_restr0.0592497
X-RAY DIFFRACTIONf_plane_restr0.007574
X-RAY DIFFRACTIONf_dihedral_angle_d24.35931237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.33251370.27972598X-RAY DIFFRACTION99.85
2.06-2.120.24291360.24112573X-RAY DIFFRACTION99.96
2.12-2.180.25811350.22152571X-RAY DIFFRACTION99.85
2.18-2.260.26761350.1972572X-RAY DIFFRACTION99.74
2.26-2.350.23741360.19032572X-RAY DIFFRACTION100
2.35-2.460.25821370.19252600X-RAY DIFFRACTION99.82
2.46-2.590.23611350.1952575X-RAY DIFFRACTION99.85
2.59-2.750.23191360.19522584X-RAY DIFFRACTION99.96
2.75-2.970.23151360.20142586X-RAY DIFFRACTION100
2.97-3.260.19571380.1812624X-RAY DIFFRACTION99.89
3.26-3.740.2171370.18032593X-RAY DIFFRACTION99.96
3.74-4.710.16531370.13712602X-RAY DIFFRACTION100
4.71-46.760.18751400.1612651X-RAY DIFFRACTION99.93

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