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- PDB-4ws2: Crystal structure of Mycobacterium tuberculosis uracil-DNA glycos... -

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Basic information

Entry
Database: PDB / ID: 4ws2
TitleCrystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 6-aminouracil, Form I
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
6-aminopyrimidine-2,4(3H,5H)-dione / CITRIC ACID / ISOPROPYL ALCOHOL / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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 1.2Apr 13, 2016Group: Data collection
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,81111
Polymers25,8141
Non-polymers99810
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.960, 64.100, 45.250
Angle α, β, γ (deg.)90.00, 112.55, 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 (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

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Non-polymers , 6 types, 348 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-6UA / 6-aminopyrimidine-2,4(3H,5H)-dione


Mass: 127.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O2
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5 / Details: Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.13→17.5 Å / Num. obs: 71969 / % possible obs: 94.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.8
Reflection shellResolution: 1.13→1.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.3 / % possible all: 90.7

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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: 1.13→17.51 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.037 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15589 3650 5.1 %RANDOM
Rwork0.12773 ---
obs0.12918 68290 94.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0.02 Å2
2--0.17 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.13→17.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 60 338 2132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191971
X-RAY DIFFRACTIONr_bond_other_d0.0010.021862
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9942711
X-RAY DIFFRACTIONr_angle_other_deg0.96634267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7735254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10921.46382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57215280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8981523
X-RAY DIFFRACTIONr_chiral_restr0.2930.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212306
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02464
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_it1.4351.012980
X-RAY DIFFRACTIONr_mcbond_other1.3991.012979
X-RAY DIFFRACTIONr_mcangle_it1.8731.5351246
X-RAY DIFFRACTIONr_mcangle_other1.8721.5351247
X-RAY DIFFRACTIONr_scbond_it1.9841.163991
X-RAY DIFFRACTIONr_scbond_other1.9831.164992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.461.681466
X-RAY DIFFRACTIONr_long_range_B_refined4.66410.4762618
X-RAY DIFFRACTIONr_long_range_B_other2.9679.0352388
X-RAY DIFFRACTIONr_rigid_bond_restr4.81133833
X-RAY DIFFRACTIONr_sphericity_free41.488555
X-RAY DIFFRACTIONr_sphericity_bonded9.56954062
LS refinement shellResolution: 1.131→1.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 264 -
Rwork0.218 4773 -
obs--89.96 %

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