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- PDB-5nnu: KSHV uracil-DNA glycosylase, product complex with dsDNA exhibitin... -

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Basic information

Entry
Database: PDB / ID: 5nnu
TitleKSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping
Components
  • DNA
  • DNA containing an abasic site
  • Uracil-DNA glycosylase
KeywordsHYDROLASE / Uracil-DNA glycosylase
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / host cell nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Uracil-DNA glycosylase / Core gene UL2 family protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsEarl, C. / Bagneris, C. / Barrett, T. / Savva, R.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping.
Authors: Earl, C. / Bagneris, C. / Zeman, K. / Cole, A. / Barrett, T. / Savva, R.
History
DepositionApr 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: DNA containing an abasic site
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase
E: Uracil-DNA glycosylase
T: DNA
U: DNA containing an abasic site
V: DNA
W: DNA containing an abasic site
X: DNA
Y: DNA containing an abasic site
Z: DNA


Theoretical massNumber of molelcules
Total (without water)135,28612
Polymers135,28612
Non-polymers00
Water2,000111
1
S: DNA containing an abasic site
A: Uracil-DNA glycosylase
T: DNA


Theoretical massNumber of molelcules
Total (without water)33,8223
Polymers33,8223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-11 kcal/mol
Surface area13190 Å2
MethodPISA
2
B: Uracil-DNA glycosylase
U: DNA containing an abasic site
V: DNA


Theoretical massNumber of molelcules
Total (without water)33,8223
Polymers33,8223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-15 kcal/mol
Surface area13260 Å2
MethodPISA
3
D: Uracil-DNA glycosylase
W: DNA containing an abasic site
X: DNA


Theoretical massNumber of molelcules
Total (without water)33,8223
Polymers33,8223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-13 kcal/mol
Surface area12880 Å2
MethodPISA
4
E: Uracil-DNA glycosylase
Y: DNA containing an abasic site
Z: DNA


Theoretical massNumber of molelcules
Total (without water)33,8223
Polymers33,8223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-13 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.100, 70.800, 140.250
Angle α, β, γ (deg.)90.000, 94.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
DNA containing an abasic site


Mass: 3230.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: AAB: DNA abasic site / Source: (synth.) synthetic construct
#2: Protein
Uracil-DNA glycosylase / UDG / UNG


Mass: 27226.174 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF46 / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Express lysY/Iq
References: UniProt: Q76RG8, UniProt: F5HFA1*PLUS, uracil-DNA glycosylase
#3: DNA chain
DNA


Mass: 3365.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.1 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, 0.1 M magnesium acetate, 8% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.97→73.09 Å / Num. obs: 33476 / % possible obs: 100 % / Redundancy: 3.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.144 / Net I/σ(I): 6.7
Reflection shellResolution: 2.97→9.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4405 / CC1/2: 0.656 / Rpim(I) all: 0.65 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHENIX1.10-2155refinement
XDSdata reduction
MOLREP11phasing
Aimless0.5.23data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J8X

2j8x


Resolution: 2.97→49.2 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.441
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2692 1717 5.3 %RANDOM
Rwork0.2438 ---
obs0.2451 32502 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 154.77 Å2 / Biso mean: 73.1692 Å2 / Biso min: 27.29 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å2-0.19 Å2
2--1.17 Å2-0 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.97→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6954 1760 0 111 8825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0179143
X-RAY DIFFRACTIONr_bond_other_d00.027435
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.77612817
X-RAY DIFFRACTIONr_angle_other_deg4317165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5545908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23421.993271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.916151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6731546
X-RAY DIFFRACTIONr_chiral_restr0.1580.21384
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218981
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021941
X-RAY DIFFRACTIONr_mcbond_it4.2496.7833650
X-RAY DIFFRACTIONr_mcbond_other4.1866.7823649
X-RAY DIFFRACTIONr_mcangle_it5.82710.0974549
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 130 -
Rwork0.339 2308 -
all-2438 -
obs--99.35 %

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