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- PDB-3a7n: Crystal structure of uracil-DNA glycosylase from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 3a7n
TitleCrystal structure of uracil-DNA glycosylase from Mycobacterium tuberculosis
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / Ung-Ugi interactions / Ung-DNA complex / citrate as protein ligand / ligand binding / inhibitor design / DNA damage / DNA repair / Glycosidase
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
CITRATE ANION / Uracil-DNA glycosylase / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKaushal, P.S. / Talawar, R.K. / Varshney, U. / Vijayan, M.
Citation
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.
#1: 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.V. / Varshney, U. / Vijayan, M.
#2: 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.
#3: 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
DepositionSep 29, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)26,1923
Polymers25,8141
Non-polymers3782
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.840, 63.670, 86.400
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 H37Rv (bacteria)
Strain: H37RV / Gene: ung, Rv2976c / Plasmid: PRSETB MTUUDG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P67071, UniProt: P9WFQ9*PLUS, uridine nucleosidase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7
Details: 1.8M tri-ammonium citrate pH 7.0, 10% isopropanol, microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2008 / Details: mirrors
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 18628 / Num. obs: 18238 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2583 / Rsym value: 0.493 / % possible all: 97.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZHX

2zhx


Resolution: 1.95→26.24 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.309 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19888 885 4.9 %RANDOM
Rwork0.18103 ---
obs0.18195 17319 97.74 %-
all-18628 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.059 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.95→26.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 26 193 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221841
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9772521
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.055232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63121.75774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80615257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5391518
X-RAY DIFFRACTIONr_chiral_restr0.070.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021453
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.2897
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21254
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3371.51200
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.59121884
X-RAY DIFFRACTIONr_scbond_it0.9193733
X-RAY DIFFRACTIONr_scangle_it1.554.5637
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 53 -
Rwork0.231 1255 -
obs--98.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.54572.105311.28151.61572.81120.1559-0.0293-0.3617-0.02110.1179-0.07080.119-0.0509-0.35580.1002-0.1022-0.01540.047-0.0240.0259-0.0104-20.6111-8.329523.3935
22.04810.26321.84690.5274-0.16332.5586-0.0547-0.05490.06110.02220.00980.1159-0.0834-0.04150.0449-0.03710.01080.0199-0.0292-0.0201-0.0147-16.8103-3.581419.4602
30.3084-0.15860.09110.43090.07220.6013-0.0109-0.0062-0.01790.00650.01390.03410.04490.0215-0.003-0.00820.0005-0.0045-0.0153-0.0061-0.0117-5.8588-13.598313.4629
41.0005-0.0396-0.12970.10730.2120.92450.0021-0.0061-0.09260.00450.0224-0.01050.0273-0.0009-0.0245-0.01090.00730.0061-0.03130.01030.00224.765-19.341711.3439
50.55220.1203-0.03320.64460.2190.0848-0.0236-0.02850.0772-0.05350.02480.0299-0.03790.0463-0.0011-0.0011-0.0068-0.0063-0.0097-0.0103-0.0222-4.0618-2.520115.1012
60.8861-0.1213-0.24070.85950.06451.1676-0.0032-0.04350.0488-0.0150.0461-0.0932-0.06310.1051-0.043-0.03770.0008-0.0013-0.0182-0.0109-0.023110.1557-8.897714.8366
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 7
2X-RAY DIFFRACTION2A8 - 41
3X-RAY DIFFRACTION3A42 - 90
4X-RAY DIFFRACTION4A91 - 125
5X-RAY DIFFRACTION5A126 - 170
6X-RAY DIFFRACTION6A171 - 227

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