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- PDB-4ws8: Crystal structure of Mycobacterium tuberculosis uracil-DNA glycos... -

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Basic information

Entry
Database: PDB / ID: 4ws8
TitleCrystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 2-thiouracil, Form V
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / DNA-repair / Excision repair / Conformational selection / Ligand-binding
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, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...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, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-thioxo-2,3-dihydropyrimidin-4(1H)-one / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsArif, S.M. / Geethanandan, K. / Mishra, P. / Surolia, A. / Varshney, U. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands.
Authors: Kaushal, P.S. / Talawar, R.K. / Varshney, U. / Vijayan, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.
Authors: Kaushal, P.S. / Talawar, R.K. / Krishna, P.D. / Varshney, U. / Vijayan, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG.
Authors: Saikrishnan, K. / Bidya Sagar, M. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M.
#4: Journal: Nucleic Acids Res. / Year: 1998
Title: X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG.
Authors: Ravishankar, R. / Bidya Sagar, M. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M.
History
DepositionOct 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,9773
Polymers25,8141
Non-polymers1642
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.060, 45.070, 122.060
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 (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ung, Rv2976c, MTCY349.11 / Plasmid: pRSETB MTUUDG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WFQ9, uracil-DNA glycosylase
#2: Chemical ChemComp-TUL / 2-thioxo-2,3-dihydropyrimidin-4(1H)-one


Mass: 128.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2OS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.6
Details: Ammonium acetate, Sodium citrate tribasic dihydrate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978565 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.4→40.69 Å / Num. obs: 41291 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 9.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A7N

3a7n


Resolution: 1.4→40.69 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.401 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16757 2072 5 %RANDOM
Rwork0.132 ---
obs0.13376 39146 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-0 Å2-0 Å2
2---0.49 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.4→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 9 211 1970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191944
X-RAY DIFFRACTIONr_bond_other_d0.0010.021848
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9752678
X-RAY DIFFRACTIONr_angle_other_deg0.8773.0014237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.645258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31721.35881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28615281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6261523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0212295
X-RAY DIFFRACTIONr_gen_planes_other00.02474
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_it1.7761.322987
X-RAY DIFFRACTIONr_mcbond_other1.7631.32986
X-RAY DIFFRACTIONr_mcangle_it2.2941.9991251
X-RAY DIFFRACTIONr_mcangle_other2.29321252
X-RAY DIFFRACTIONr_scbond_it3.631.678957
X-RAY DIFFRACTIONr_scbond_other3.6291.678958
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9392.3871423
X-RAY DIFFRACTIONr_long_range_B_refined4.69712.4932419
X-RAY DIFFRACTIONr_long_range_B_other4.12111.9562338
X-RAY DIFFRACTIONr_rigid_bond_restr2.47233792
X-RAY DIFFRACTIONr_sphericity_free34.478582
X-RAY DIFFRACTIONr_sphericity_bonded9.80153859
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 158 -
Rwork0.261 2843 -
obs--100 %

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