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- PDB-8i62: Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycos... -

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Basic information

Entry
Database: PDB / ID: 8i62
TitleCrystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Barbituric acid, 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
BARBITURIC ACID / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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)26,0755
Polymers25,8141
Non-polymers2614
Water6,612367
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, 63.910, 45.280
Angle α, β, γ (deg.)90.00, 112.70, 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-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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
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
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→36.24 Å / Num. obs: 55586 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Net I/σ(I): 14
Reflection shellResolution: 1.26→1.32 Å / Rmerge(I) obs: 0.221 / Num. unique obs: 7932 / CC1/2: 0.948

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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: 1.26→36.26 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.295 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14319 2616 4.7 %RANDOM
Rwork0.10899 ---
obs0.11059 52947 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.861 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.82 Å2
2---0.37 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.26→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 15 367 2121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131912
X-RAY DIFFRACTIONr_bond_other_d0.0140.0171777
X-RAY DIFFRACTIONr_angle_refined_deg2.0221.6432632
X-RAY DIFFRACTIONr_angle_other_deg1.7091.5654103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.79819.01101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98515277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7081522
X-RAY DIFFRACTIONr_chiral_restr0.1230.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022262
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02444
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_it5.7321.551975
X-RAY DIFFRACTIONr_mcbond_other5.7221.55974
X-RAY DIFFRACTIONr_mcangle_it5.4952.3361238
X-RAY DIFFRACTIONr_mcangle_other5.4932.3371239
X-RAY DIFFRACTIONr_scbond_it4.7381.801937
X-RAY DIFFRACTIONr_scbond_other4.7361.804938
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0092.5641395
X-RAY DIFFRACTIONr_long_range_B_refined6.58620.5192283
X-RAY DIFFRACTIONr_long_range_B_other6.27619.1882190
X-RAY DIFFRACTIONr_rigid_bond_restr9.49433689
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.26→1.29 Å
RfactorNum. reflection% reflection
Rfree0.206 193 -
Rwork0.151 3781 -
obs--95.97 %

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