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- PDB-6iob: The structure of the H109A mutant of UdgX in complex with uracil -

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Basic information

Entry
Database: PDB / ID: 6iob
TitleThe structure of the H109A mutant of UdgX in complex with uracil
ComponentsPhage SPO1 DNA polymerase-related protein
KeywordsDNA BINDING PROTEIN / 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 speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 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 1.1Mar 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: Phage SPO1 DNA polymerase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8803
Polymers22,4161
Non-polymers4642
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-21 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.151, 51.158, 40.957
Angle α, β, γ (deg.)90.00, 92.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phage SPO1 DNA polymerase-related protein


Mass: 22416.490 Da / Num. of mol.: 1 / Fragment: UNP residues 7-215 / Mutation: H109A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: mc2155 / Gene: MSMEI_0259 / Production host: Escherichia coli (E. coli) / References: UniProt: I7F541, DNA-directed DNA polymerase
#2: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.83 Å3/Da / Density % sol: 32.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.15M Sodium malonate pH 7.0 and 3.8% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 11019 / % possible obs: 97.4 % / Observed criterion σ(I): 3 / Redundancy: 5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.102 / Net I/σ(I): 14
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3 / Num. unique obs: 1072 / CC1/2: 0.958 / % possible all: 97.8

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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 / Resolution: 2.002→31.959 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.9
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 482 4.93 %RANDOM
Rwork0.1946 ---
obs0.1973 9782 88.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→31.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 16 99 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131578
X-RAY DIFFRACTIONf_angle_d1.8742145
X-RAY DIFFRACTIONf_dihedral_angle_d15.965936
X-RAY DIFFRACTIONf_chiral_restr0.096243
X-RAY DIFFRACTIONf_plane_restr0.015284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0025-2.29220.26151360.19342557X-RAY DIFFRACTION74
2.2922-2.88760.25021850.21593373X-RAY DIFFRACTION98
2.8876-31.96260.25451610.18493370X-RAY DIFFRACTION95

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