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

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Basic information

Entry
Database: PDB / ID: 4dof
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: 2.8 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)109,0124
Polymers109,0124
Non-polymers00
Water1,42379
1
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)54,5062
Polymers54,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)54,5062
Polymers54,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)27,2531
Polymers27,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)27,2531
Polymers27,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)27,2531
Polymers27,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)27,2531
Polymers27,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.200, 102.880, 117.240
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: 27253.119 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% PEG 8000, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Jul 3, 2011 / 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: 2.8→19.85 Å / Num. all: 27886 / Num. obs: 27886 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 7.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2740 / Rsym value: 0.381 / % possible all: 99.9

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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: 2.8→19.85 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.883 / SU B: 35.182 / SU ML: 0.326 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26939 1395 5 %RANDOM
Rwork0.22119 ---
all0.22364 26255 --
obs0.22364 26255 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7080 0 0 79 7159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.027243
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9519856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3035868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48724.232319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.901151231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8511528
X-RAY DIFFRACTIONr_chiral_restr0.0760.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215452
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 90 -
Rwork0.321 1761 -
obs-1761 99.84 %
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)
11.8235-0.5863-0.28234.1978-0.01221.81850.00330.1295-0.0081-0.0602-0.19580.1046-0.0345-0.00220.19250.05570.0182-0.01010.15080.01570.0273-21.90923.523-21.914
23.6085-0.6399-0.55432.51730.42261.27670.1451-0.0803-0.07870.1422-0.0566-0.20190.0374-0.0981-0.08860.16360.00960.0190.06920.01320.0406-47.009-2.422-9.503
31.40820.8869-0.47645.28270.30451.7028-0.16020.06140.05540.2460.12120.2311-0.0320.06320.03910.06460.0232-0.00670.16650.02510.082-25.76622.22520.758
44.82581.4645-0.91132.017-0.62071.2612-0.007-0.0066-0.0916-0.0614-0.0268-0.0188-0.09540.05180.03370.1681-0.01420.0860.0527-0.02010.0571-0.856-1.8497.111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 218
2X-RAY DIFFRACTION2B1 - 218
3X-RAY DIFFRACTION3C1 - 218
4X-RAY DIFFRACTION4D1 - 218

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