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- PDB-4qca: Crystal structure of Vaccinia virus uracil-DNA glycosylase mutant... -

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Basic information

Entry
Database: PDB / ID: 4qca
TitleCrystal structure of Vaccinia virus uracil-DNA glycosylase mutant R167AD4
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / DNA repair enzyme / component of processivity factor / A20 / DNA / Poxvirus
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSartmatova, D. / Nash, T. / Schormann, N. / Nuth, M. / Ricciardi, R. / Banerjee, S. / Chattopadhyay, D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization and preliminary X-ray diffraction analysis of three recombinant mutants of Vaccinia virus uracil DNA glycosylase.
Authors: Sartmatova, D. / Nash, T. / Schormann, N. / Nuth, M. / Ricciardi, R. / Banerjee, S. / Chattopadhyay, D.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Source and taxonomy
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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
B: Uracil-DNA glycosylase
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,66113
Polymers101,1124
Non-polymers5499
Water9,764542
1
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7586
Polymers50,5562
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9037
Polymers50,5562
Non-polymers3475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.140, 118.268, 121.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Uracil-DNA glycosylase / UDG


Mass: 25277.914 Da / Num. of mol.: 4 / Mutation: D17N, R167A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Western Reserve, D4R, VACWR109 / Gene: ACAM3000_MVA_101, D4, MVA101R, UNG / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: Q91UM2, UniProt: P04303*PLUS, uracil-DNA glycosylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 2:1:1 protein solution/water/reservoir (unbuffered 16% PEG3350, 0.15 M potassium fluoride, 10% glycerol), pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2012 / Details: Mirrors
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→46.57 Å / Num. all: 80549 / Num. obs: 80549 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.9 / Num. unique all: 11684 / Rsym value: 0.597 / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
RAPDdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DOF, CHAIN A

4dof


Resolution: 1.9→42.45 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.544 / SU ML: 0.105 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.164 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 4036 5 %RANDOM
Rwork0.2044 ---
all0.206 80488 --
obs0.206 80488 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.92 Å2 / Biso mean: 24.52 Å2 / Biso min: 11.29 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7111 0 29 542 7682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197341
X-RAY DIFFRACTIONr_bond_other_d0.0010.026954
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9529985
X-RAY DIFFRACTIONr_angle_other_deg0.757316064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76724.255322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.783151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9991527
X-RAY DIFFRACTIONr_chiral_restr0.0690.21105
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218145
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021680
X-RAY DIFFRACTIONr_mcbond_it0.9812.3623527
X-RAY DIFFRACTIONr_mcbond_other0.9812.3623526
X-RAY DIFFRACTIONr_mcangle_it1.6723.5374404
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 302 -
Rwork0.255 5583 -
all-5885 -
obs-5885 97.39 %

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