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- PDB-6lye: Crystal Structure of mimivirus UNG Y322F in complex with UGI -

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Basic information

Entry
Database: PDB / ID: 6lye
TitleCrystal Structure of mimivirus UNG Y322F in complex with UGI
Components
  • Probable uracil-DNA glycosylase
  • Uracil-DNA glycosylase inhibitor
KeywordsDNA BINDING PROTEIN/INHIBITOR / UDG / UNG / uracil DNA glycosylase / UGI / DNA BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
Similarity search - Function
Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like ...Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / 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 / Nuclear Transport Factor 2; Chain: A, / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase inhibitor / Probable uracil-DNA glycosylase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
Bacillus phage PBS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPathak, D. / Kwon, E. / Kim, D.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017R1A6A3A11029218 Korea, Republic Of
National Research Foundation (NRF, Korea)2017R1D1A1B03034088 Korea, Republic Of
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Selective interactions between mimivirus uracil-DNA glycosylase and inhibitory proteins determined by a single amino acid.
Authors: Pathak, D. / Kwon, E. / Kim, D.Y.
History
DepositionFeb 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Nov 29, 2023Group: 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: Probable uracil-DNA glycosylase
I: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)41,1832
Polymers41,1832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-10 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.230, 104.230, 83.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Probable uracil-DNA glycosylase / UDG


Mass: 31831.734 Da / Num. of mol.: 1 / Mutation: Y322F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: UNG, MIMI_L249 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5UPT2, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Protein Uracil-DNA glycosylase inhibitor


Mass: 9351.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage PBS2 (virus) / Gene: UGI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14739

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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: 3.16 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 16.75% (v/v) PEG3350, 8% (v/v) PEG400, and 0.1 M sodium acetate/acetic acid pH 5.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.34
ReflectionResolution: 3.1→45.133 Å / Num. obs: 9163 / % possible obs: 97.6 % / Redundancy: 4.25 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.3
Reflection shellResolution: 3.1→3.31 Å / Rmerge(I) obs: 0.604 / Num. unique obs: 1685

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Processing

Software
NameVersionClassification
PHENIXdev_3051refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X55

5x55


Resolution: 3.1→45.133 Å / Cross valid method: THROUGHOUT / σ(F): 79.49 / Phase error: 25 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2085 469 5.13 %
Rwork0.1732 8642 -
obs0.1868 9136 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.15 Å2 / Biso mean: 75.172 Å2 / Biso min: 39.46 Å2
Refinement stepCycle: final / Resolution: 3.1→45.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 0 0 2851
Num. residues----353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1025-3.55080.29331590.25082838299792
3.5508-4.47130.2471310.19252944307594
4.4713-30.090.18571750.15692860303590

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