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- PDB-6ioa: The structure of UdgX in complex with uracil -

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Basic information

Entry
Database: PDB / ID: 6ioa
TitleThe structure 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 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)24,9324
Polymers24,3731
Non-polymers5603
Water2,072115
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 area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.407, 51.448, 55.430
Angle α, β, γ (deg.)90.00, 105.48, 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-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.05M MES pH 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→24.65 Å / Num. obs: 10655 / % possible obs: 98.4 % / Observed criterion σ(I): 4.3 / Redundancy: 2.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.9
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1707 / CC1/2: 0.869 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IO9

6io9


Resolution: 2.15→24.65 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.076 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.188 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21211 500 4.7 %RANDOM
Rwork0.16288 ---
obs0.16529 10151 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.15 Å2
2---0.42 Å20 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.15→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 21 115 1654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191572
X-RAY DIFFRACTIONr_bond_other_d0.0070.021503
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.992138
X-RAY DIFFRACTIONr_angle_other_deg1.9223.0023436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33322.76965
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71515235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3661516
X-RAY DIFFRACTIONr_chiral_restr0.120.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211794
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3651.233827
X-RAY DIFFRACTIONr_mcbond_other1.3661.231826
X-RAY DIFFRACTIONr_mcangle_it2.2611.8411032
X-RAY DIFFRACTIONr_mcangle_other2.2611.8431033
X-RAY DIFFRACTIONr_scbond_it1.851.342745
X-RAY DIFFRACTIONr_scbond_other1.8361.33742
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.931.9491089
X-RAY DIFFRACTIONr_long_range_B_refined4.58810.0711752
X-RAY DIFFRACTIONr_long_range_B_other4.63410.0761753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 35 -
Rwork0.161 716 -
obs--95.79 %

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