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- PDB-6ajq: E52Q mutant form of Uracil DNA glycosylase X from Mycobacterium s... -

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Basic information

Entry
Database: PDB / ID: 6ajq
TitleE52Q mutant form of Uracil DNA glycosylase X from Mycobacterium smegmatis.
ComponentsUracil DNA glycosylase superfamily protein
KeywordsDNA BINDING PROTEIN / DNA repair / Base excision / DNA-Protein crosslink.
Function / homology
Function and homology information


uracil DNA N-glycosylase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding
Similarity search - Function
Uracil-DNA glycosylase family 4 / : / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / 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
IRON/SULFUR CLUSTER / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.342 Å
AuthorsAhn, W.C. / Aroli, S. / Varshney, U. / Woo, E.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2018R1A2A2A05021648 Korea, Republic Of
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision.
Authors: Ahn, W.C. / Aroli, S. / Kim, J.H. / Moon, J.H. / Lee, G.S. / Lee, M.H. / Sang, P.B. / Oh, B.H. / Varshney, U. / Woo, E.J.
History
DepositionAug 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5522
Polymers22,2001
Non-polymers3521
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-20 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.395, 51.602, 54.436
Angle α, β, γ (deg.)90.00, 105.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uracil DNA glycosylase superfamily protein


Mass: 22200.297 Da / Num. of mol.: 1 / Mutation: E52Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEG_0265 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0QP43
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 2.0M ammonium citrate tribasic pH7.0, 0.1M Bis-Tris propane pH7.0

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 41987 / % possible obs: 96.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 33.05
Reflection shellResolution: 1.34→1.36 Å / Rmerge(I) obs: 0.383 / Num. unique obs: 2098

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.342→18.4 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.62
RfactorNum. reflection% reflection
Rfree0.1909 2006 4.78 %
Rwork0.1734 --
obs0.1743 41956 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.342→18.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 8 244 1802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071604
X-RAY DIFFRACTIONf_angle_d0.9252186
X-RAY DIFFRACTIONf_dihedral_angle_d10.548939
X-RAY DIFFRACTIONf_chiral_restr0.086246
X-RAY DIFFRACTIONf_plane_restr0.006291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3423-1.37580.24581360.23552761X-RAY DIFFRACTION94
1.3758-1.4130.25491470.22092941X-RAY DIFFRACTION100
1.413-1.45460.24461450.20352945X-RAY DIFFRACTION100
1.4546-1.50150.19221560.19122938X-RAY DIFFRACTION100
1.5015-1.55510.21841420.1782924X-RAY DIFFRACTION100
1.5551-1.61740.17721490.16522944X-RAY DIFFRACTION100
1.6174-1.69090.19241340.16352944X-RAY DIFFRACTION100
1.6909-1.780.17011600.1652943X-RAY DIFFRACTION100
1.78-1.89140.17891430.15772920X-RAY DIFFRACTION99
1.8914-2.03730.17571470.15852954X-RAY DIFFRACTION99
2.0373-2.2420.16891450.15962917X-RAY DIFFRACTION99
2.242-2.56570.17821470.1672905X-RAY DIFFRACTION98
2.5657-3.22960.18921460.1712841X-RAY DIFFRACTION95
3.2296-18.40140.21281090.192073X-RAY DIFFRACTION68

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