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- PDB-8i67: Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycos... -

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Basic information

Entry
Database: PDB / ID: 8i67
TitleCrystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 2,4-Thiazolidinedione, Form I
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
1,3-thiazolidine-2,4-dione / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsRaj, P. / Paul, A. / Gopal, B.
Funding support1items
OrganizationGrant numberCountry
Other government
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)25,9933
Polymers25,8141
Non-polymers1792
Water5,567309
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)39.280, 63.410, 45.440
Angle α, β, γ (deg.)90.00, 112.80, 90.00
Int Tables number4
Space group name H-MP1211

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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-OD3 / 1,3-thiazolidine-2,4-dione / 2,4-Thiazolidinedione


Mass: 117.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H3NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 25% PEG (w/v) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→34.95 Å / Num. obs: 20377 / % possible obs: 94 % / Redundancy: 2.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Net I/σ(I): 6.7
Reflection shellResolution: 1.72→1.82 Å / Rmerge(I) obs: 0.21 / Num. unique obs: 2829 / CC1/2: 0.941

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WS4

4ws4


Resolution: 1.72→34.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.043 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24009 1052 5.2 %RANDOM
Rwork0.18415 ---
obs0.1869 19162 92.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.278 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20.37 Å2
2--0.7 Å2-0 Å2
3----1.07 Å2
Refinement stepCycle: 1 / Resolution: 1.72→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 11 309 2054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131825
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171701
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.6452498
X-RAY DIFFRACTIONr_angle_other_deg1.3611.5653922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32418.96997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6991521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
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_it1.0811.55920
X-RAY DIFFRACTIONr_mcbond_other1.0781.549919
X-RAY DIFFRACTIONr_mcangle_it1.6122.3231151
X-RAY DIFFRACTIONr_mcangle_other1.6122.3241152
X-RAY DIFFRACTIONr_scbond_it1.5731.695905
X-RAY DIFFRACTIONr_scbond_other1.5731.696906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3412.4771346
X-RAY DIFFRACTIONr_long_range_B_refined4.34119.8792123
X-RAY DIFFRACTIONr_long_range_B_other4.01218.9032040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.724→1.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 74 -
Rwork0.196 1344 -
obs--88.9 %

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