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- PDB-1q3f: Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-c... -

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Basic information

Entry
Database: PDB / ID: 1q3f
TitleUracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA
Components
  • 5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3'
  • 5'-D(*TP*GP*TP*(NRI)P*AP*TP*CP*TP*T)-3'
  • Uracil-DNA glycosylase
KeywordsHYDROLASE/DNA / UDG / DNA repair / 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
PHOSPHATE ION / URACIL / DNA / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBianchet, M.A. / Seiple, L.A. / Jiang, Y.L. / Ichikawa, Y. / Amzel, L.M. / Stivers, J.T.
CitationJournal: Biochemistry / Year: 2003
Title: Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase.
Authors: Bianchet, M.A. / Seiple, L.A. / Jiang, Y.L. / Ichikawa, Y. / Amzel, L.M. / Stivers, J.T.
History
DepositionJul 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 7, 2015Group: Structure summary
Revision 1.4Aug 16, 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_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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The NRI and URA is a transition state analog. This transition state analog has an uracil ...HETEROGEN The NRI and URA is a transition state analog. This transition state analog has an uracil and a modified deoxyribose that are not covalently connected to each other.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*TP*GP*TP*(NRI)P*AP*TP*CP*TP*T)-3'
C: 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)31,4085
Polymers31,2013
Non-polymers2072
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.640, 65.890, 99.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules BC

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


Mass: 2586.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 1-aza-2'-deoxyribose-containing DNA
#2: DNA chain 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

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Protein , 1 types, 1 molecules A

#3: Protein Uracil-DNA glycosylase / 3.2.2.- / 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 OR DGU OR UNG15 / Production host: Escherichia coli (E. coli)
References: UniProt: P13051, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 3 types, 277 molecules

#4: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 4000, 10% dioxane, 100mM Hepes , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2dioxane11
3Hepes11
4H2O11
5PEG 400012
6dioxane12
7Hepes12
8H2O12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 mMdithiothreitol1reservoir
218 %PEG40001reservoir
310 %dioxane1reservoir
4100 mMHEPES1reservoirpH6.5
58.8 mg/mlhUDG1drop
61 mMDNA1drop
70.5 mMuracil1drop
81

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 22, 2003 / 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: 1.9→36.51 Å / Num. obs: 24682 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.245 / % possible all: 69.1
Reflection
*PLUS
Lowest resolution: 36.5 Å / Rmerge F obs: 0.06
Reflection shell
*PLUS
% possible obs: 69.1 % / Rmerge(I) obs: 0.25

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AKX

1akx


Resolution: 1.9→36.52 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 2383 9.2 %RANDOM
Rwork0.1903 ---
obs0.1903 24682 93 %-
Refinement stepCycle: LAST / Resolution: 1.9→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 375 13 275 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006608
X-RAY DIFFRACTIONc_angle_d1.33519
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.5442
X-RAY DIFFRACTIONc_scbond_it1.8472
X-RAY DIFFRACTIONc_scangle_it2.8092.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Rfactor Rfree: 0.235 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3

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