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- PDB-8i6b: Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycos... -

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Basic information

Entry
Database: PDB / ID: 8i6b
TitleCrystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, 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
5-oxidanyl-1~{H}-pyrimidine-2,4-dione / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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)26,52412
Polymers25,8141
Non-polymers71011
Water5,044280
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)39.160, 63.680, 45.190
Angle α, β, γ (deg.)90.00, 112.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 291 molecules

#2: Chemical ChemComp-ODF / 5-oxidanyl-1~{H}-pyrimidine-2,4-dione / 5-Hydroxy-2,4(1H,3H)-pyrimidinedion


Mass: 128.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O3
#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 38.97 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5 / Details: 0.1 M Tris pH 5.5, 25% PEG (w/v) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30.49 Å / Num. obs: 25418 / % possible obs: 93.72 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.0368 / Net I/σ(I): 11.77
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.1443 / Num. unique obs: 2415 / CC1/2: 0.927

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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: 1.6→30.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 1196 4.7 %RANDOM
Rwork0.14902 ---
obs0.15057 24223 93.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.572 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å20.14 Å2
2--0.17 Å20 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.6→30.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 37 280 2056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131840
X-RAY DIFFRACTIONr_bond_other_d0.0340.0171728
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.6492517
X-RAY DIFFRACTIONr_angle_other_deg2.3081.5643977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3355236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18619.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90215260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2971520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022099
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02415
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_it1.0030.999926
X-RAY DIFFRACTIONr_mcbond_other0.9950.999925
X-RAY DIFFRACTIONr_mcangle_it1.5591.4971159
X-RAY DIFFRACTIONr_mcangle_other1.5591.4981160
X-RAY DIFFRACTIONr_scbond_it1.7861.184914
X-RAY DIFFRACTIONr_scbond_other1.7851.186915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.71.6871356
X-RAY DIFFRACTIONr_long_range_B_refined4.64213.3732177
X-RAY DIFFRACTIONr_long_range_B_other4.39312.5072102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 88 -
Rwork0.216 1693 -
obs--88.83 %

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