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- PDB-5nnh: KSHV uracil-DNA glycosylase, apo form -

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Basic information

Entry
Database: PDB / ID: 5nnh
TitleKSHV uracil-DNA glycosylase, apo form
ComponentsUracil-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 / base-excision repair / host cell nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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
Uracil-DNA glycosylase / Core gene UL2 family protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEarl, C. / Bagneris, C. / Cole, A.R. / Barrett, T. / Savva, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust099765/Z/12/Z United Kingdom
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 9, 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 1.3Oct 9, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_CC_half
Revision 1.4Jan 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

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3222
Polymers27,2261
Non-polymers961
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.201, 53.811, 40.811
Angle α, β, γ (deg.)90.000, 93.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uracil-DNA glycosylase / / UDG / UNG


Mass: 27226.174 Da / Num. of mol.: 1
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) / Strain (production host): T7 Express lysY/Iq
References: UniProt: Q76RG8, UniProt: F5HFA1*PLUS, uracil-DNA glycosylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.3 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M bis-tris, 0.2 M lithium sulfate monohydrate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 2.2→52.63 Å / Num. obs: 11700 / % possible obs: 100 % / Redundancy: 16.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.204 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 15 % / Rmerge(I) obs: 0.567 / Num. unique obs: 1027 / CC1/2: 0.858 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
DIALS1.3data reduction
Aimless0.5.23data scaling
PHASER2.7.16phasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J8X

2j8x


Resolution: 2.2→52.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.22
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 442 3.8 %RANDOM
Rwork0.194 ---
obs0.196 11642 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.91 Å2 / Biso mean: 50.2919 Å2 / Biso min: 28.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.03 Å2
2--1.73 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→52.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 5 80 1825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191796
X-RAY DIFFRACTIONr_bond_other_d00.021625
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9462456
X-RAY DIFFRACTIONr_angle_other_deg3.82533742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6715224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89522.60969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04915267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4911510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211978
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02384
X-RAY DIFFRACTIONr_mcbond_it1.1592.405902
X-RAY DIFFRACTIONr_mcbond_other1.1582.404901
X-RAY DIFFRACTIONr_mcangle_it1.9963.5951124
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.257 876 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: -14.948 Å / Origin y: 10.559 Å / Origin z: 4.864 Å
111213212223313233
T0.0871 Å20.0319 Å2-0.1249 Å2-0.0548 Å20.0359 Å2--0.3379 Å2
L2.9093 °21.1196 °21.5239 °2-6.2118 °20.5374 °2--1.1641 °2
S-0.0334 Å °-0.0932 Å °-0.1624 Å °0.1895 Å °0.0134 Å °-0.5296 Å °0.0543 Å °0.0877 Å °0.0199 Å °

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