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- PDB-2owq: Crystal structure of vaccinia virus uracil-DNA glycosylase -

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Basic information

Entry
Database: PDB / ID: 2owq
TitleCrystal structure of vaccinia virus uracil-DNA glycosylase
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / Uracil-DNA Glycosylase Fold in the Core: 3 layers (a/b/a) / and parallel beta-sheet of 4 strands in the order 2134 / Novel Features: Beta-Sheets at N- and C-terminus
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / DNA repair / DNA binding
Similarity search - Function
Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Uracil-DNA glycosylase / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.4 Å
AuthorsSchormann, N. / Chattopadhyay, D.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly
Authors: Schormann, N. / Grigorian, A. / Samal, A. / Krishnan, R. / DeLucas, L. / Chattopadhyay, D.
History
DepositionFeb 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jun 29, 2016Group: Source and taxonomy
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,21311
Polymers54,5062
Non-polymers7079
Water2,630146
1
A: Uracil-DNA glycosylase
hetero molecules

A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,03810
Polymers54,5062
Non-polymers5318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2
B: Uracil-DNA glycosylase
hetero molecules

B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,38912
Polymers54,5062
Non-polymers88310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Unit cell
Length a, b, c (Å)85.197, 85.197, 139.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 2

Dom-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA-1 - 21819 - 238
2BB-8 - 21812 - 238
DetailsThe asymmetric unit contains two chains related by non-crystallographic symmetry. The biological assembly is likely a dimer generated from each chain by space group symmetry operations. The second part of the biological assembly of chain A is generated by the space group symmetry operation: y, x, -z. The second part of the biological assembly of chain B is generated by the space group symmetry operation: -x, y-x, 2/3-z.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 27253.119 Da / Num. of mol.: 2 / Mutation: D17N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Genus: Orthopoxvirus / Gene: D4R, VACWR109 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS Rosetta
References: UniProt: Q91UM2, UniProt: P04303*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 5 types, 155 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 1.5 M ammonium sulfate, 12% glycerol, 0.1M Hepes, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 2, 2005 / Details: Osmic Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→19.96 Å / Num. all: 23203 / Num. obs: 23203 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.68 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.299 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.3.0011refinement
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→19.27 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.882 / SU B: 21.213 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2995 1194 5.2 %RANDOM
Rwork0.2407 ---
all0.2436 23150 --
obs0.2436 21956 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 45 146 3705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223667
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9624974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08224.268157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97415613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.181514
X-RAY DIFFRACTIONr_chiral_restr0.080.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022749
X-RAY DIFFRACTIONr_nbd_refined0.1980.21704
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2181
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.27
X-RAY DIFFRACTIONr_mcbond_it0.2651.52269
X-RAY DIFFRACTIONr_mcangle_it0.46323596
X-RAY DIFFRACTIONr_scbond_it0.50931618
X-RAY DIFFRACTIONr_scangle_it0.8324.51377
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A835tight positional0.180.05
1B849medium positional0.50.5
2A835tight thermal0.290.5
2B849medium thermal0.442
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 98 -
Rwork0.295 1601 -
obs-1699 99.65 %
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)
12.64271.7162-0.14593.3452-0.24722.62460.33180.05480.10520.3655-0.18970.29940.4267-0.6948-0.1422-0.0166-0.2665-0.0189-0.0010.0632-0.0761-36.725-26.555-11.123
22.90661.3943-0.10413.5539-0.54372.4170.4619-0.2802-0.03110.5534-0.3727-0.06870.2725-0.4019-0.08920.0652-0.3174-0.0497-0.0430.0312-0.126-30.436-23.726-5.317
32.92062.0213-0.64194.5562-0.40773.93530.4691-0.4286-0.20931.0728-0.456-0.19070.14530.0835-0.01310.1461-0.2654-0.0922-0.15680.0928-0.0443-20.947-18.564-2.411
43.70420.449-1.29290.7718-0.34923.4567-0.00090.2304-0.1560.13090.02040.01360.2636-0.1736-0.0195-0.2518-0.0337-0.006-0.10390.0894-0.0937-15.44-16.496-32.742
53.55090.7136-0.74141.4694-0.21982.3024-0.03310.4552-0.12550.00110.11450.04780.1399-0.0141-0.0814-0.2944-0.0157-0.01820.05460.0887-0.1178-9.81-13.466-39.016
64.2567-0.12640.6842.148-0.125.06230.12380.3838-0.0377-0.16620.1431-0.1445-0.05020.2957-0.2669-0.2897-0.041-0.02510.08610.1173-0.0526-1.048-7.523-42.503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 9721 - 117
2X-RAY DIFFRACTION2AA98 - 162118 - 182
3X-RAY DIFFRACTION3AA163 - 218183 - 238
4X-RAY DIFFRACTION4BB1 - 9721 - 117
5X-RAY DIFFRACTION5BB98 - 162118 - 182
6X-RAY DIFFRACTION6BB163 - 218183 - 238

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