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- PDB-6ajp: Complex form of Uracil DNA glycosylase X and deoxyuridine monopho... -

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Basic information

Entry
Database: PDB / ID: 6ajp
TitleComplex form of Uracil DNA glycosylase X and deoxyuridine monophosphate.
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
2'-DEOXYURIDINE-5'-MONOPHOSPHATE / IRON/SULFUR CLUSTER / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.334 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 20, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_src_syn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil DNA glycosylase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0323
Polymers24,3731
Non-polymers6602
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-20 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.436, 51.209, 54.533
Angle α, β, γ (deg.)90.00, 104.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uracil DNA glycosylase superfamily protein


Mass: 24372.654 Da / Num. of mol.: 1 / Fragment: UNP residues 7-215
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-DU / 2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P / Details: Deoxyuridine monophosphate
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: 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: 2.21 Å3/Da / Density % sol: 39 %
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: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 43215 / % possible obs: 96.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 47.76
Reflection shellResolution: 1.33→1.35 Å / Rmerge(I) obs: 0.153 / Num. unique obs: 1511

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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: 1.334→18.877 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.66
RfactorNum. reflection% reflection
Rfree0.1873 1995 4.62 %
Rwork0.1629 --
obs0.164 43193 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.334→18.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 28 244 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111591
X-RAY DIFFRACTIONf_angle_d1.22169
X-RAY DIFFRACTIONf_dihedral_angle_d25.066574
X-RAY DIFFRACTIONf_chiral_restr0.082244
X-RAY DIFFRACTIONf_plane_restr0.007285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3341-1.36750.23711130.21182627X-RAY DIFFRACTION87
1.3675-1.40450.22421560.20012960X-RAY DIFFRACTION100
1.4045-1.44580.22271470.19462961X-RAY DIFFRACTION100
1.4458-1.49240.18781440.18082998X-RAY DIFFRACTION100
1.4924-1.54570.1971380.17782983X-RAY DIFFRACTION99
1.5457-1.60760.19691510.16522973X-RAY DIFFRACTION99
1.6076-1.68070.17371400.15852992X-RAY DIFFRACTION99
1.6807-1.76930.17551510.15552942X-RAY DIFFRACTION99
1.7693-1.880.17311420.15353010X-RAY DIFFRACTION100
1.88-2.0250.17761500.15423038X-RAY DIFFRACTION100
2.025-2.22850.17541380.15262985X-RAY DIFFRACTION100
2.2285-2.55030.1841430.15673034X-RAY DIFFRACTION100
2.5503-3.21060.19171530.16193013X-RAY DIFFRACTION100
3.2106-18.8790.1911290.16612682X-RAY DIFFRACTION87

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