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- PDB-1emj: URACIL-DNA GLYCOSYLASE BOUND TO DNA CONTAINING A 4'-THIO-2'DEOXYU... -

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Basic information

Entry
Database: PDB / ID: 1emj
TitleURACIL-DNA GLYCOSYLASE BOUND TO DNA CONTAINING A 4'-THIO-2'DEOXYURIDINE ANALOG PRODUCT
Components
  • DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*(ASU)P*AP*TP*CP*TP*T)-3')
  • URACIL-DNA GLYCOSYLASE
Keywordshydrolase/DNA / alpha/beta fold / Uracil-DNA Glycosylase / protein/DNA / 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 / single strand break repair / 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 ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / single strand break repair / 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
URACIL / DNA / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsParikh, S.S. / Walcher, G. / Jones, G.D. / Slupphaug, G. / Krokan, H.E. / Blackburn, G.M. / Tainer, J.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
Authors: Parikh, S.S. / Walcher, G. / Jones, G.D. / Slupphaug, G. / Krokan, H.E. / Blackburn, G.M. / Tainer, J.A.
#1: Journal: Embo J. / Year: 1998
Title: Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA
Authors: Parikh, S.S. / Mol, C.D. / Slupphaug, G. / Krokan, H.E. / Tainer, J.A.
History
DepositionMar 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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
B: DNA (5'-D(*TP*GP*TP*(ASU)P*AP*TP*CP*TP*T)-3')
C: DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3')
A: URACIL-DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3464
Polymers31,2343
Non-polymers1121
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.554, 64.853, 96.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*TP*GP*TP*(ASU)P*AP*TP*CP*TP*T)-3')


Mass: 2619.762 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3')


Mass: 3070.071 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein URACIL-DNA GLYCOSYLASE / E.C.3.2.2.3


Mass: 25544.137 Da / Num. of mol.: 1 / Mutation: RESIDUES 85-304
Source method: isolated from a genetically manipulated source
Details: MITOCHONDRIAL PROTEIN / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13051, uridine nucleosidase
#4: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, HEPES buffer, NaCl, dioxane, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES buffer11
2NaCl11
3dioxane11
4DTT11
5PEG 400011
6PEG 400012
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG40001reservoir
2100 mMHEPES1reservoir
310 %1reservoir
41 mMdithiothreitol1reservoir
51
61

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 18, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 21503 / Num. obs: 21491 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.99 % / Biso Wilson estimate: 19.44 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.464 / Num. unique all: 2088 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 150204
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2042 10 %random
Rwork0.228 ---
all-21111 --
obs-21107 99.9 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 376 8 161 2353
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.48

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