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- PDB-3tkb: crystal structure of human uracil-DNA glycosylase D183G/K302R mutant -

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Basic information

Entry
Database: PDB / ID: 3tkb
Titlecrystal structure of human uracil-DNA glycosylase D183G/K302R mutant
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / glycosidase / alpha/beta protein
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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
IMIDAZOLE / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAssefa, N.G. / Niiranen, L. / Willassen, N.P. / Smalas, A.O. / Moe, E.
CitationJournal: Comp.Biochem.Physiol. B: Biochem.Mol.Biol. / Year: 2012
Title: Thermal unfolding studies of cold adapted uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). A comparative study with human UNG.
Authors: Assefa, N.G. / Niiranen, L. / Willassen, N.P. / Smalas, A. / Moe, E.
History
DepositionAug 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
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)25,6523
Polymers25,5141
Non-polymers1382
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.530, 39.710, 66.730
Angle α, β, γ (deg.)90.000, 97.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uracil-DNA glycosylase / / UDG


Mass: 25514.115 Da / Num. of mol.: 1 / Fragment: catalytical domain, UNP residues 94-313 / Mutation: D183G, K302R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNG, DGU, UNG1, UNG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P13051, uracil-DNA glycosylase
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 18% PEG 4000, 0.041M ammonium sulfate, 0.05M sodium chloride, 0.1M imidazole/maleate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.399→34.04 Å / Num. all: 30634 / Num. obs: 30527 / % possible obs: 69.6 % / Observed criterion σ(I): 3 / Redundancy: 3.567 % / Biso Wilson estimate: 18.012 Å2 / Rmerge(I) obs: 0.021 / Net I/σ(I): 42.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.582.30.04117.8455519510.04138.4
1.58-1.682.50.03918.4740430050.03962.6
1.68-1.792.90.03519.41124838940.03585.7
1.79-1.9440.02823.31695842840.02899.4
1.94-2.124.20.02328.21636139300.023100
2.12-2.374.20.0232.11491735770.02100
2.37-2.744.20.01833.31326131760.018100
2.74-3.354.20.01832.41124027020.018100
3.35-4.744.10.01833.4843220790.01899.2
4.74-34.043.80.01538418410940.01591.4

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AKZ

1akz


Resolution: 1.5→34.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8987 / SU B: 1.042 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0845 / SU Rfree: 0.0882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1464 4.9 %RANDOM
Rwork0.1515 ---
obs0.1535 29680 83.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.02 Å2 / Biso mean: 12.8287 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.08 Å2
2--0.13 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 10 343 2159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211980
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9362700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3745246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80523.69692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2315328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.017159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211578
X-RAY DIFFRACTIONr_mcbond_it0.931.51183
X-RAY DIFFRACTIONr_mcangle_it1.50621929
X-RAY DIFFRACTIONr_scbond_it2.3353797
X-RAY DIFFRACTIONr_scangle_it3.8364.5771
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 47 -
Rwork0.163 797 -
all-844 -
obs--32.32 %

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