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- PDB-8iie: Complex form of MsmUdgX and uracil- obtained from uracil DNA (ttU... -

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Basic information

Entry
Database: PDB / ID: 8iie
TitleComplex form of MsmUdgX and uracil- obtained from uracil DNA (ttUtt) post its cleavage by MsmUdgX
ComponentsType-4 uracil-DNA glycosylase
KeywordsDNA BINDING PROTEIN / UdgX / Uracil / Complex / DNA
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: 1.67 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)22,2803
Polymers21,8161
Non-polymers4642
Water2,522140
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 area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.420, 51.330, 55.140
Angle α, β, γ (deg.)90.00, 104.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Type-4 uracil-DNA glycosylase


Mass: 21815.777 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
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: Sep 17, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.67→29.02 Å / Num. obs: 22686 / % possible obs: 98 % / Redundancy: 4.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.04 / Rrim(I) all: 0.064 / Net I/σ(I): 17.9
Reflection shellResolution: 1.67→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 864 / CC1/2: 0.598 / Rpim(I) all: 0.251 / Rrim(I) all: 0.383 / % possible all: 75.1

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
PHASERphasing
Aimlessdata scaling
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→23.64 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 16.3 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1879 1168 5.16 %
Rwork0.1583 --
obs0.1598 22622 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 0 140 1672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171592
X-RAY DIFFRACTIONf_angle_d1.3992164
X-RAY DIFFRACTIONf_dihedral_angle_d7.071227
X-RAY DIFFRACTIONf_chiral_restr0.11246
X-RAY DIFFRACTIONf_plane_restr0.013287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.750.23051650.19522618X-RAY DIFFRACTION98
1.75-1.840.23091430.19172624X-RAY DIFFRACTION98
1.84-1.960.19071560.14512628X-RAY DIFFRACTION99
1.96-2.110.17241530.1462677X-RAY DIFFRACTION99
2.11-2.320.16761380.14432703X-RAY DIFFRACTION100
2.32-2.650.18841250.15812715X-RAY DIFFRACTION100
2.65-3.340.20951270.16212744X-RAY DIFFRACTION100
3.34-23.640.1721610.15672745X-RAY DIFFRACTION100

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