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- PDB-6l5a: The structure of the UdgX mutant H109E at a pre-excision state -

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Basic information

Entry
Database: PDB / ID: 6l5a
TitleThe structure of the UdgX mutant H109E at a pre-excision state
ComponentsUracil DNA glycosylase superfamily protein
KeywordsDNA BINDING PROTEIN / UdgX / covalent complex / protein-DNA interaction / DNA repair / glycosylase
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 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.80007323734 Å
AuthorsXie, W. / Tu, J. / Zeng, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870782 China
CitationJournal: DNA Repair (Amst) / Year: 2021
Title: Structural insights into an MsmUdgX mutant capable of both crosslinking and uracil excision capability.
Authors: Jia, Q. / Zeng, H. / Tu, J. / Sun, L. / Cao, W. / Xie, W.
History
DepositionOct 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: Uracil DNA glycosylase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7854
Polymers23,2491
Non-polymers5363
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-20 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.698, 48.316, 86.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Uracil DNA glycosylase superfamily protein


Mass: 23249.420 Da / Num. of mol.: 1 / Mutation: H109E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEG_0265 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QP43
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 19% PEG3350, 0.1 M sodium citrate, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→21.56 Å / Num. obs: 18687 / % possible obs: 98.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 8.78342573865 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 8.4 / Num. unique obs: 2586 / CC1/2: 0.985 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IO9

6io9


Resolution: 1.80007323734→21.55545 Å / SU ML: 0.155071477148 / Cross valid method: FREE R-VALUE / σ(F): 1.3379521463 / Phase error: 17.4976843893
RfactorNum. reflection% reflection
Rfree0.192672984964 920 4.93774151997 %
Rwork0.151306999552 --
obs0.153380596451 18632 97.6366399413 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.6844359257 Å2
Refinement stepCycle: LAST / Resolution: 1.80007323734→21.55545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 20 268 1824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215408590191588
X-RAY DIFFRACTIONf_angle_d1.667501348752155
X-RAY DIFFRACTIONf_chiral_restr0.0565940780818243
X-RAY DIFFRACTIONf_plane_restr0.00594241724132286
X-RAY DIFFRACTIONf_dihedral_angle_d18.4341084538948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.89490.2079602308161070.1413917192762417X-RAY DIFFRACTION94.3904263276
1.8949-2.01360.1907280895421190.1443383078142531X-RAY DIFFRACTION98.4764028242
2.0136-2.16890.1918246950921200.1419650659812533X-RAY DIFFRACTION99.3632958801
2.1689-2.38690.1839012977651450.1495350527322544X-RAY DIFFRACTION99.261720192
2.3869-2.73170.2185650982421230.1608990581912566X-RAY DIFFRACTION99.1884913316
2.7317-3.43940.2096093571141310.1578753600092580X-RAY DIFFRACTION98.4029038113
3.4394-21.5550.1737667934251750.1517873176052541X-RAY DIFFRACTION94.6011842564

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