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- PDB-5nn7: KSHV uracil-DNA glycosylase, apo form -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5nn7
TitleKSHV uracil-DNA glycosylase, apo form
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / Uracil-DNA glycosylase
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / 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
Uracil-DNA glycosylase / Core gene UL2 family protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 8, 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
A: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)26,8251
Polymers26,8251
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.873, 43.038, 57.387
Angle α, β, γ (deg.)90.000, 99.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26824.758 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M bis-tris, 0.2 M sodium chloride, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→56.63 Å / Num. obs: 7316 / % possible obs: 100 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.051 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 6.9 / Num. unique all: 809 / CC1/2: 0.978 / Rpim(I) all: 0.125

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHENIX1.10-2155refinement
PDB_EXTRACT3.1data extraction
DIALS1.3data reduction
Aimless0.5.23data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J8X

2j8x


Resolution: 2.5→56.63 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.331
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 323 4.4 %RANDOM
Rwork0.2056 ---
obs0.2074 7306 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.21 Å2 / Biso mean: 22.6685 Å2 / Biso min: 11.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0 Å21.31 Å2
2---1.83 Å2-0 Å2
3---2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.5→56.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 0 74 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191904
X-RAY DIFFRACTIONr_bond_other_d00.021758
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.952592
X-RAY DIFFRACTIONr_angle_other_deg3.5134068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38122.80582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11215312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0711514
X-RAY DIFFRACTIONr_chiral_restr0.0420.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212087
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02407
X-RAY DIFFRACTIONr_mcbond_it2.1292.2930
X-RAY DIFFRACTIONr_mcbond_other2.132.197929
X-RAY DIFFRACTIONr_mcangle_it2.8813.2751159
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 31 -
Rwork0.249 503 -
all-534 -
obs--99.63 %

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