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- PDB-6ail: CRYSTAL STRUCTURE AT 1.3 ANGSTROMS RESOLUTION OF A NOVEL UDG, Udg... -

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Basic information

Entry
Database: PDB / ID: 6ail
TitleCRYSTAL STRUCTURE AT 1.3 ANGSTROMS RESOLUTION OF A NOVEL UDG, UdgX, FROM Mycobacterium smegmatis
ComponentsUracil DNA glycosylase X
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 str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.335 Å
AuthorsAhn, W.C. / Aroli, S. / Varshney, V. / 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 24, 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 X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7242
Polymers24,3731
Non-polymers3521
Water3,423190
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 area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.326, 51.638, 54.362
Angle α, β, γ (deg.)90.00, 105.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uracil DNA glycosylase X


Mass: 24372.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Asp165, Asp166, and Pro209 could not be modeled.
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: MC2 155 / 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.: 190 / 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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 291 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: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.335→50 Å / Num. obs: 42217 / % possible obs: 96.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 55.74
Reflection shellResolution: 1.34→1.36 Å / Rmerge(I) obs: 0.187 / Num. unique obs: 1864

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data collection
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.335→28.106 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1557 2002 4.74 %
Rwork0.1325 --
obs0.1336 42199 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.335→28.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 8 190 1732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091576
X-RAY DIFFRACTIONf_angle_d0.9322137
X-RAY DIFFRACTIONf_dihedral_angle_d20.638576
X-RAY DIFFRACTIONf_chiral_restr0.074241
X-RAY DIFFRACTIONf_plane_restr0.007282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3351-1.36850.16861240.12622427X-RAY DIFFRACTION81
1.3685-1.40550.15491390.11762866X-RAY DIFFRACTION95
1.4055-1.44690.16351430.1142837X-RAY DIFFRACTION96
1.4469-1.49360.13731380.11212862X-RAY DIFFRACTION96
1.4936-1.54690.15161450.10862869X-RAY DIFFRACTION96
1.5469-1.60890.14571410.10092899X-RAY DIFFRACTION97
1.6089-1.68210.13651450.10412901X-RAY DIFFRACTION97
1.6821-1.77080.1281470.11352907X-RAY DIFFRACTION97
1.7708-1.88170.13291490.11352932X-RAY DIFFRACTION98
1.8817-2.02690.15571450.11622969X-RAY DIFFRACTION98
2.0269-2.23080.15111480.1252935X-RAY DIFFRACTION98
2.2308-2.55350.1371450.13492969X-RAY DIFFRACTION99
2.5535-3.21640.16331450.15412998X-RAY DIFFRACTION99
3.2164-28.11220.18841480.16882826X-RAY DIFFRACTION92

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