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- PDB-6lyd: Crystal Structure of mimivirus UNG Y322L in complex with UGI -

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Basic information

Entry
Database: PDB / ID: 6lyd
TitleCrystal Structure of mimivirus UNG Y322L 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-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...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-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / 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: 2.598 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)41,1492
Polymers41,1492
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-11 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.766, 103.766, 81.523
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: 31797.719 Da / Num. of mol.: 1 / Mutation: Y322L
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) / Strain (production host): BL21(DE3)
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) / Strain (production host): BL21(DE3) / References: UniProt: P14739
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 10% PEG 8000 (v/v), 40 mM potassium phosphate monobasic, 20% glycerol (v/v), and 0.2 uL of 5% ethyl acetate (v/v)

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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 PILATUS 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
ReflectionResolution: 2.598→50 Å / Num. obs: 15494 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 30.6
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.458 / Num. unique obs: 770

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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: 2.598→32.053 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1509 10.02 %
Rwork0.1698 13552 -
obs0.1756 15061 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.93 Å2 / Biso mean: 42.7332 Å2 / Biso min: 21 Å2
Refinement stepCycle: final / Resolution: 2.598→32.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 0 131 2986
Biso mean---40.36 -
Num. residues----354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.598-2.68170.36411360.2336116493
2.6817-2.77750.28891330.2162116694
2.7775-2.88870.26711380.2175121996
2.8887-3.02010.31131330.2151120596
3.0201-3.17910.28051380.2094120697
3.1791-3.37810.23451350.1933124597
3.3781-3.63860.25691320.1709124498
3.6386-4.00420.21021410.1613126699
4.0042-4.58210.19241330.13381270100
4.5821-5.76750.18681440.13931267100
5.7675-32.0530.17351460.15081300100

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