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- PDB-2oyt: Crystal Structure of UNG2/DNA(TM) -

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Basic information

Entry
Database: PDB / ID: 2oyt
TitleCrystal Structure of UNG2/DNA(TM)
Components
  • DNA strand1
  • DNA strand2
  • Uracil-DNA glycosylase
Keywordshydrolase/DNA / Enzyme-DNA complex / UNG2 / hydrolase-DNA COMPLEX
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 superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / 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 superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / 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
DNA / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBianchet, M.A. / Krosky, D.J. / Stivers, J.T. / Amzel, L.M.
CitationJournal: Nature / Year: 2007
Title: Enzymatic capture of an extrahelical thymine in the search for uracil in DNA.
Authors: Parker, J.B. / Bianchet, M.A. / Krosky, D.J. / Friedman, J.I. / Amzel, L.M. / Stivers, J.T.
History
DepositionFeb 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 9, 2014Group: Non-polymer description
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 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_conn / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: DNA strand1
C: DNA strand2


Theoretical massNumber of molelcules
Total (without water)31,2143
Polymers31,2143
Non-polymers00
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.499, 66.318, 100.316
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: 25544.137 Da / Num. of mol.: 1
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, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: DNA chain DNA strand1


Mass: 2603.696 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA strand2


Mass: 3066.118 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 52.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Recombinat human UNG2 (22 mg/ml) in 50 mM tris-OAc buffer pH 7.0, 150 mM NaCl and 1mM DTT was mixed with T/M DNA duplex (2.5 mM) inclubate at room T for 30 min and then centrifugate at 10000 ...Details: Recombinat human UNG2 (22 mg/ml) in 50 mM tris-OAc buffer pH 7.0, 150 mM NaCl and 1mM DTT was mixed with T/M DNA duplex (2.5 mM) inclubate at room T for 30 min and then centrifugate at 10000 g for 5 min. Co-crystallization conditions 22-25% PEG 4000, 10mM Hepes pH 6.5, 1mM DTT, 0.5 % v/v dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1tris-OAc buffer11
2NaCl11
3DTT11
4PEG 400011
5Hepes11
6dioxane11
7PEG 400012
8Hepes12
9dioxane12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2006 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→36.47 Å / Num. obs: 20504 / % possible obs: 90.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 29.9 Å2 / Rsym value: 0.066 / Net I/σ(I): 43.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 6.36 / Rsym value: 0.247 / % possible all: 55.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMH

1emh


Resolution: 2→36.47 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.872 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1019 5 %RANDOM
Rwork0.192 ---
all0.194 ---
obs0.194 20446 90.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.728 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å20 Å2
2--0.72 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 376 0 398 2582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212290
X-RAY DIFFRACTIONr_angle_refined_deg1.2092.1433165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1725222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60523.70889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37615307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.85158
X-RAY DIFFRACTIONr_chiral_restr0.0660.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021640
X-RAY DIFFRACTIONr_nbd_refined0.170.21076
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2367
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.230
X-RAY DIFFRACTIONr_mcbond_it0.3531.51144
X-RAY DIFFRACTIONr_mcangle_it0.59221796
X-RAY DIFFRACTIONr_scbond_it0.77731418
X-RAY DIFFRACTIONr_scangle_it1.2414.51369
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 49 -
Rwork0.208 837 -
obs-886 54.22 %

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