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- PDB-6io9: The structure of apo-UdgX -

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Basic information

Entry
Database: PDB / ID: 6io9
TitleThe structure of apo-UdgX
ComponentsPhage SPO1 DNA polymerase-related protein
KeywordsHYDROLASE / uracil DNA glycosylase / DNA repair / iron-sulfur
Function / homology
Function and homology information


uracil DNA N-glycosylase activity / nucleotidyltransferase 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXie, W. / Tu, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870782 China
National Natural Science Foundation of China31700657 China
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation.
Authors: Tu, J. / Chen, R. / Yang, Y. / Cao, W. / Xie, W.
History
DepositionOct 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Phage SPO1 DNA polymerase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8203
Polymers24,3731
Non-polymers4482
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-20 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.572, 50.958, 54.367
Angle α, β, γ (deg.)90.00, 104.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phage SPO1 DNA polymerase-related 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: MSMEI_0259 / Production host: Escherichia coli (E. coli) / References: UniProt: I7F541
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.01 Å3/Da / Density % sol: 38.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6 / Details: 0.05M MES 5.6, 2.45M (NH4)2SO4 and 0.1M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 15400 / % possible obs: 97.2 % / Observed criterion σ(I): 4.7 / Redundancy: 3.4 % / CC1/2: 0.98 / Rmerge(I) obs: 0.093 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1486 / CC1/2: 0.84 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UI0

1ui0


Resolution: 1.9→36.606 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.08
RfactorNum. reflection% reflection
Rfree0.2252 752 5.03 %
Rwork0.1899 --
obs0.1917 14942 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→36.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 13 96 1625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011563
X-RAY DIFFRACTIONf_angle_d1.6332129
X-RAY DIFFRACTIONf_dihedral_angle_d17.205922
X-RAY DIFFRACTIONf_chiral_restr0.058244
X-RAY DIFFRACTIONf_plane_restr0.007281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8991-2.04570.2511470.19162810X-RAY DIFFRACTION97
2.0457-2.25150.25851440.19062789X-RAY DIFFRACTION96
2.2515-2.57730.25681560.20172842X-RAY DIFFRACTION98
2.5773-3.24680.25961500.21342839X-RAY DIFFRACTION97
3.2468-36.6130.19171550.17582910X-RAY DIFFRACTION97

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