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- PDB-8iip: Complex form of MsmUdgX H109Q mutant and uracil- obtained from ur... -

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Basic information

Entry
Database: PDB / ID: 8iip
TitleComplex form of MsmUdgX H109Q mutant and uracil- obtained from uracil DNA (ttUtt) post its cleavage by MsmUdgX H109Q
ComponentsType-4 uracil-DNA glycosylase
KeywordsDNA BINDING PROTEIN / UdgX / H109Q / 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
BETA-MERCAPTOETHANOL / IRON/SULFUR CLUSTER / URACIL / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 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 1.1Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 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)22,3484
Polymers21,8061
Non-polymers5423
Water2,828157
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 area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.560, 51.340, 54.880
Angle α, β, γ (deg.)90.00, 104.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Type-4 uracil-DNA glycosylase


Mass: 21805.758 Da / Num. of mol.: 1 / Mutation: H109Q
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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
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: Apr 20, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.63→28.13 Å / Num. obs: 24686 / % possible obs: 100 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.055 / Rrim(I) all: 0.088 / Net I/σ(I): 12.7
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1270 / CC1/2: 0.684 / Rpim(I) all: 0.42 / Rrim(I) all: 0.672 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→23.58 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 18.68 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2027 1234 5 %
Rwork0.1756 --
obs0.177 24670 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→23.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 20 157 1680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061594
X-RAY DIFFRACTIONf_angle_d0.9252168
X-RAY DIFFRACTIONf_dihedral_angle_d5.726229
X-RAY DIFFRACTIONf_chiral_restr0.067247
X-RAY DIFFRACTIONf_plane_restr0.007288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.70.31381310.30282583X-RAY DIFFRACTION100
1.7-1.770.22541270.21982591X-RAY DIFFRACTION100
1.77-1.870.20691280.17282619X-RAY DIFFRACTION100
1.87-1.980.19341200.16842614X-RAY DIFFRACTION100
1.98-2.140.22061390.18052596X-RAY DIFFRACTION100
2.14-2.350.20281480.16572578X-RAY DIFFRACTION100
2.35-2.690.21841420.17152598X-RAY DIFFRACTION100
2.69-3.390.19461590.17152585X-RAY DIFFRACTION100
3.39-23.580.1771400.15992672X-RAY DIFFRACTION100

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