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- PDB-6ioc: The structure of the H109Q mutant of UdgX in complex with uracil -

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Basic information

Entry
Database: PDB / ID: 6ioc
TitleThe structure of the H109Q mutant of UdgX in complex with uracil
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 / URACIL / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.624 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)22,9373
Polymers22,4741
Non-polymers4642
Water2,630146
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 area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.683, 50.711, 38.826
Angle α, β, γ (deg.)90.00, 90.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phage SPO1 DNA polymerase-related protein


Mass: 22473.541 Da / Num. of mol.: 1 / Fragment: UNP residues 7-215 / Mutation: H109Q
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, DNA-directed DNA polymerase
#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-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.69 Å3/Da / Density % sol: 27.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2.15M Sodium malonate pH 7.0 and 3.8% MPD / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 18944 / % possible obs: 99.5 % / Observed criterion σ(I): 3.8 / Redundancy: 6 % / CC1/2: 0.973 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.9
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 914 / CC1/2: 0.876 / % possible all: 99.9

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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: 6IOA

6ioa


Resolution: 1.624→30.827 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.35
RfactorNum. reflection% reflection
Rfree0.1817 838 4.6 %
Rwork0.1549 --
obs0.1561 18216 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.624→30.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 16 146 1725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121615
X-RAY DIFFRACTIONf_angle_d2.0142196
X-RAY DIFFRACTIONf_dihedral_angle_d17.647960
X-RAY DIFFRACTIONf_chiral_restr0.063246
X-RAY DIFFRACTIONf_plane_restr0.007294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6235-1.72520.24811010.18842451X-RAY DIFFRACTION82
1.7252-1.85840.21651140.16432899X-RAY DIFFRACTION95
1.8584-2.04540.19791670.15462946X-RAY DIFFRACTION98
2.0454-2.34130.1971570.15153005X-RAY DIFFRACTION100
2.3413-2.94940.19491440.16173025X-RAY DIFFRACTION99
2.9494-30.83230.1431550.14443052X-RAY DIFFRACTION99

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