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- PDB-6ajs: H109S mutant form of Uracil DNA glycosylase X. -

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Basic information

Entry
Database: PDB / ID: 6ajs
TitleH109S mutant form of Uracil DNA glycosylase X.
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: 1.632 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)22,5022
Polymers22,1501
Non-polymers3521
Water3,891216
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 area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.229, 51.393, 54.444
Angle α, β, γ (deg.)90.00, 105.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uracil DNA glycosylase superfamily protein


Mass: 22150.213 Da / Num. of mol.: 1 / Mutation: H109S
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.: 216 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
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: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 23431 / % possible obs: 97.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 56
Reflection shellResolution: 1.63→1.66 Å / Rmerge(I) obs: 0.129 / Num. unique obs: 1101

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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: 1.632→28.022 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.38
RfactorNum. reflection% reflection
Rfree0.1971 2003 8.56 %
Rwork0.1599 --
obs0.163 23412 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.632→28.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 8 216 1762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071576
X-RAY DIFFRACTIONf_angle_d0.9372145
X-RAY DIFFRACTIONf_dihedral_angle_d10.513952
X-RAY DIFFRACTIONf_chiral_restr0.06242
X-RAY DIFFRACTIONf_plane_restr0.006285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6319-1.67270.19261210.14471385X-RAY DIFFRACTION88
1.6727-1.7180.1941460.14361560X-RAY DIFFRACTION100
1.718-1.76850.20361620.14151545X-RAY DIFFRACTION100
1.7685-1.82560.18611310.14471603X-RAY DIFFRACTION100
1.8256-1.89080.20411550.14371530X-RAY DIFFRACTION100
1.8908-1.96650.20371410.14541598X-RAY DIFFRACTION100
1.9665-2.0560.18361510.14671536X-RAY DIFFRACTION100
2.056-2.16430.18771480.14941560X-RAY DIFFRACTION99
2.1643-2.29990.18971470.15211554X-RAY DIFFRACTION99
2.2999-2.47740.21281430.15651594X-RAY DIFFRACTION100
2.4774-2.72650.20681530.16411562X-RAY DIFFRACTION100
2.7265-3.12060.19171400.16971557X-RAY DIFFRACTION99
3.1206-3.92980.1871460.15651538X-RAY DIFFRACTION96
3.9298-28.02660.2091190.18951287X-RAY DIFFRACTION79

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