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- PDB-8iii: Complex form of MsmUdgX H109C mutant and uracil- obtained from ur... -

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Basic information

Entry
Database: PDB / ID: 8iii
TitleComplex form of MsmUdgX H109C mutant and uracil- obtained from uracil DNA (ttUtt) post its cleavage by MsmUdgX H109C
ComponentsType-4 uracil-DNA glycosylase
KeywordsDNA BINDING PROTEIN / UdgX / H109C / Uracil / Complex / protein
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 / : / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily
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 / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsAroli, S.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR28058 India
Department of Biotechnology (DBT, India)BT/PR13522 India
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Mutational and structural analyses of UdgX: insights into the active site pocket architecture and its evolution.
Authors: Aroli, S. / Woo, E.J. / Gopal, B. / Varshney, U.
History
DepositionFeb 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type-4 uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2664
Polymers21,7101
Non-polymers5563
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-20 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.480, 51.370, 54.990
Angle α, β, γ (deg.)90.00, 104.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Type-4 uracil-DNA glycosylase


Mass: 21709.693 Da / Num. of mol.: 1 / Mutation: H109C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEG_0265 / Plasmid: pET14b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0QP43, uracil-DNA glycosylase
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7
Details: 2.0M Ammonium citrate tribasic pH7.0, 0.1M BIS-TRIS propane pH7.0
PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.72→28.12 Å / Num. obs: 18866 / % possible obs: 89.7 % / Redundancy: 3.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.083 / Rrim(I) all: 0.119 / Net I/σ(I): 7.4
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1117 / CC1/2: 0.721 / Rpim(I) all: 0.499 / Rrim(I) all: 0.718 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→26.47 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 23.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2325 944 5.02 %
Rwork0.2011 --
obs0.2027 18791 89.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 22 131 1646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081592
X-RAY DIFFRACTIONf_angle_d1.0132162
X-RAY DIFFRACTIONf_dihedral_angle_d6.353229
X-RAY DIFFRACTIONf_chiral_restr0.066246
X-RAY DIFFRACTIONf_plane_restr0.009286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.810.32231440.27972810X-RAY DIFFRACTION100
1.81-1.920.30991440.26292235X-RAY DIFFRACTION86
1.93-2.070.21441180.19692199X-RAY DIFFRACTION87
2.09-2.280.29861030.2692345X-RAY DIFFRACTION88
2.28-2.610.23561530.18622815X-RAY DIFFRACTION100
2.61-3.290.20351380.18112732X-RAY DIFFRACTION95
3.29-26.470.19741440.16982711X-RAY DIFFRACTION93

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