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- PDB-3eug: CRYSTAL STRUCTURE OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE AND ... -

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Basic information

Entry
Database: PDB / ID: 3eug
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE AND ITS COMPLEXES WITH URACIL AND GLYCEROL: STRUCTURE AND GLYCOSYLASE MECHANISM REVISITED
ComponentsPROTEIN (GLYCOSYLASE)
KeywordsHYDROLASE / GLYCOSYLASE
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / cytoplasm
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
Uracil-DNA glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsXiao, G. / Tordova, M. / Jagadeesh, J. / Drohat, A.C. / Stivers, J.T. / Gilliland, G.L.
CitationJournal: Proteins / Year: 1999
Title: Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited.
Authors: Xiao, G. / Tordova, M. / Jagadeesh, J. / Drohat, A.C. / Stivers, J.T. / Gilliland, G.L.
History
DepositionOct 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.6Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLYCOSYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8653
Polymers25,6811
Non-polymers1842
Water6,251347
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.850, 58.930, 63.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (GLYCOSYLASE) / UDG / UNG


Mass: 25681.107 Da / Num. of mol.: 1 / Mutation: Y19H
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN IS COMPLEXED WITH URACIL / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Description: SIGMA CHEMICAL / Gene: UNG / Production host: Escherichia coli (E. coli) / References: UniProt: P12295, uridine nucleosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growpH: 8.5
Details: PROTEIN CONCENTRATION 14.9 MG/ML, 0.2 M SODIUM ACETATE, 30% PEG4000, 0.1 M TRIS BUFFER, PH 8.5 USING HANGING DROP AT 293K.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114.9 mg/mlprotein1drop
20.2 Msodium acetate1reservoir
330 %PEG40001reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER / Wavelength: 1.5418
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: Aug 1, 1997
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→99 Å / Num. obs: 32361 / % possible obs: 97 % / Observed criterion σ(I): 1.5 / Redundancy: 5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.8
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.4 / % possible all: 91.1
Reflection
*PLUS
Highest resolution: 1.43 Å / Num. obs: 39441 / % possible obs: 90 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.073

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
X-GENdata reduction
X-GENdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EUG

1eug


Resolution: 1.43→99 Å / Num. parameters: 8639 / Num. restraintsaints: 7478 / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
all0.162 36241 -
obs--92.4 %
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2155
Refinement stepCycle: LAST / Resolution: 1.43→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 12 347 2147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 99 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.026

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