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- PDB-8i63: Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycos... -

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Basic information

Entry
Database: PDB / ID: 8i63
TitleCrystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Barbituric acid, Form III
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE/INHIBITOR / DNA repair / Base excision repair / Inhibitor-complex / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / cytoplasm
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily
Similarity search - Domain/homology
BARBITURIC ACID / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRaj, P. / Paul, A. / Gopal, B.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
Citation
Journal: Eur.J.Med.Chem. / Year: 2023
Title: Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the ...Title: Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the barbituric acid fragment.
Authors: Kesharwani, S. / Raj, P. / Paul, A. / Roy, K. / Bhanot, A. / Mehta, A. / Gopal, A. / Varshney, U. / Gopal, B. / Sundriyal, S.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2015
Title: Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications.
Authors: Arif, S.M. / Geethanandan, K. / Mishra, P. / Surolia, A. / Varshney, U. / Vijayan, M.
History
DepositionJan 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0664
Polymers25,8141
Non-polymers2523
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.380, 59.700, 73.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 25813.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: ung, Rv2976c, MTCY349.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFQ9, uracil-DNA glycosylase
#2: Chemical ChemComp-BR8 / BARBITURIC ACID


Mass: 128.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1.98 Å3/Da / Density % sol: 37.72 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG 3350

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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: Aug 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.95→28.84 Å / Num. obs: 15145 / % possible obs: 97.9 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Net I/σ(I): 8.01
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.4025 / Num. unique obs: 1449 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WRV

4wrv


Resolution: 1.95→28.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.822 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21886 719 4.7 %RANDOM
Rwork0.17599 ---
obs0.17809 14426 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.181 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å2-0 Å2
2---0.65 Å20 Å2
3---1.32 Å2
Refinement stepCycle: 1 / Resolution: 1.95→28.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 17 130 1833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131776
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171669
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6462431
X-RAY DIFFRACTIONr_angle_other_deg1.2961.5653842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43318.92593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03915251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1211520
X-RAY DIFFRACTIONr_chiral_restr0.0710.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02408
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_it2.3292.89894
X-RAY DIFFRACTIONr_mcbond_other2.3222.889893
X-RAY DIFFRACTIONr_mcangle_it3.5074.3161118
X-RAY DIFFRACTIONr_mcangle_other3.5064.3171119
X-RAY DIFFRACTIONr_scbond_it2.9233.214882
X-RAY DIFFRACTIONr_scbond_other2.9223.217883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6494.6691313
X-RAY DIFFRACTIONr_long_range_B_refined7.1735.6992065
X-RAY DIFFRACTIONr_long_range_B_other7.16635.5282045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 46 -
Rwork0.291 1020 -
obs--95.26 %

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