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- PDB-4dog: Structures of Vaccinia Virus Uracil-DNA Glycosylase in New Crysta... -

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Basic information

Entry
Database: PDB / ID: 4dog
TitleStructures of Vaccinia Virus Uracil-DNA Glycosylase in New Crystal Forms
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / DNA BINDING COMPONENT / VIRAL PROCESSIVITY FACTOR / Glycosidase / DNA repair
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
Uracil-DNA glycosylase / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchormann, N. / Chattopadhyay, D.
CitationJournal: To be Published
Title: Analysis of the Dimer Interface in Crystal Structures of Vaccinia Virus Uracil DNA Glycosylase
Authors: Schormann, N. / Sommers, C.I. / Ricciardi, R.P. / Chattopadhyay, D.
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Source and taxonomy
Revision 1.2Sep 13, 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)25,5223
Polymers25,3641
Non-polymers1582
Water43224
1
A: Uracil-DNA glycosylase
hetero molecules

A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0446
Polymers50,7282
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2760 Å2
ΔGint-35 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.790, 85.790, 123.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 25364.029 Da / Num. of mol.: 1 / Mutation: D17N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: D4R, VACWR109 / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS Rosetta
References: UniProt: Q91UM2, UniProt: P04303*PLUS, uracil-DNA glycosylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M Ammonium sulfate, 10% Glycerol, 0.1M Hepes, 10mM Nickel sulfate, pH 7.5, 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: Sep 1, 2010 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→19.93 Å / Num. all: 11573 / Num. obs: 11573 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2322 / Rsym value: 0.369 / % possible all: 94

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.6.0117refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OWQ

2owq


Resolution: 2.3→19.55 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 20.937 / SU ML: 0.235 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.378 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27573 555 4.8 %RANDOM
Rwork0.23431 ---
all0.23623 11016 --
obs0.23623 11016 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.731 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0.67 Å2-0 Å2
2---1.35 Å20 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 9 24 1774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021797
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9522442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8885213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49624.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44215302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.25157
X-RAY DIFFRACTIONr_chiral_restr0.0820.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211350
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 32 -
Rwork0.318 709 -
obs-741 93.21 %
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)
15.1073-2.4258-1.33854.7537-2.4783.9573-0.04520.78130.2526-0.55940.00990.04810.38110.11810.03530.3374-0.0923-0.05160.8160.00890.31337.1775-16.6995-22.166
26.1043-0.3161-1.79421.94880.10822.3853-0.13780.0696-0.1059-0.28680.173-0.05370.28620.2375-0.03520.1819-0.0287-0.03590.4136-0.16210.112730.4713-16.5871-12.7572
36.1265-0.2698-1.39391.86070.21271.9427-0.1654-0.3495-0.0297-0.06710.24290.15310.22560.0704-0.07740.1324-0.0269-0.05950.394-0.11430.140120.8092-15.3145-6.2055
411.50660.972-1.48521.5668-1.55335.44180.216-1.38560.85130.08130.15680.21340.0560.3156-0.37280.0535-0.0072-0.06230.5248-0.28390.39916.5746-8.22931.2027
58.71543.0386-1.300512.7841-1.55673.51750.0731.07541.1506-0.31580.23710.5993-0.1569-0.5951-0.31010.1172-0.079-0.10120.50360.12080.4638.4367-7.6164-12.6265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 11
2X-RAY DIFFRACTION2A12 - 83
3X-RAY DIFFRACTION3A84 - 161
4X-RAY DIFFRACTION4A162 - 202
5X-RAY DIFFRACTION5A203 - 218

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