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- PDB-4ws7: Crystal structure of Mycobacterium tuberculosis uracil-DNA glycos... -

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Basic information

Entry
Database: PDB / ID: 4ws7
TitleCrystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-chlorouracil, Form II
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
5-chloropyrimidine-2,4(1H,3H)-dione / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 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: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_keywords
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_oper_list.symmetry_operation / _struct_keywords.text
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)26,0584
Polymers25,8141
Non-polymers2443
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.370, 43.780, 67.230
Angle α, β, γ (deg.)90.00, 98.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21A-497-

HOH

31A-501-

HOH

41A-503-

HOH

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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-5UC / 5-chloropyrimidine-2,4(1H,3H)-dione


Mass: 146.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3ClN2O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 293 K / Method: microbatch
Details: Potassium bromide, Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.88→36.91 Å / Num. obs: 16412 / % possible obs: 99.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.6
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6

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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: 1.88→36.91 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.842 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18187 830 5.1 %RANDOM
Rwork0.14158 ---
obs0.14362 15579 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å2-0.68 Å2
2---0.22 Å20 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.88→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 14 238 1956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191802
X-RAY DIFFRACTIONr_bond_other_d0.0020.021705
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.9732473
X-RAY DIFFRACTIONr_angle_other_deg0.97233909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3625232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63421.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66315252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8461519
X-RAY DIFFRACTIONr_chiral_restr0.1130.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
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_it1.4231.43916
X-RAY DIFFRACTIONr_mcbond_other1.4231.429915
X-RAY DIFFRACTIONr_mcangle_it2.2032.1351149
X-RAY DIFFRACTIONr_mcangle_other2.2022.1361150
X-RAY DIFFRACTIONr_scbond_it2.3141.683886
X-RAY DIFFRACTIONr_scbond_other2.3131.683886
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5682.4241324
X-RAY DIFFRACTIONr_long_range_B_refined5.78712.9272228
X-RAY DIFFRACTIONr_long_range_B_other5.51912.3512137
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 57 -
Rwork0.317 1137 -
obs--99.17 %

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