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- PDB-4eug: Crystallographic and Enzymatic Studies of an Active Site Variant ... -

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Basic information

Entry
Database: PDB / ID: 4eug
TitleCrystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil Complex
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 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 glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsXiao, G. / Tordova, M. / Drohat, A.C. / Jagadeesh, J. / Stivers, J.T. / Gilliland, G.L.
CitationJournal: Biochemistry / Year: 1999
Title: Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187.
Authors: Drohat, A.C. / Xiao, G. / Tordova, M. / Jagadeesh, J. / Pankiewicz, K.W. / Watanabe, K.A. / Gilliland, G.L. / Stivers, J.T.
History
DepositionDec 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 23, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Sep 13, 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)


Theoretical massNumber of molelcules
Total (without water)25,6961
Polymers25,6961
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.100, 59.000, 63.800
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: 25696.117 Da / Num. of mol.: 1 / Mutation: H187Q
Source method: isolated from a genetically manipulated source
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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
Details: Xiao, G., (1999) Proteins Struct.Funct.Genet., 35, 13.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114.9 mg/mlprotein1drop
20.2 Msodium acetate1reservoir
330 %PEG40001reservoir
40.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.95
DetectorType: BRUKER / Detector: CCD / Date: Jul 15, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.4→99 Å / Num. obs: 77493 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 18.7
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EUG

3eug


Resolution: 1.4→99 Å / Num. parameters: 8359 / Num. restraintsaints: 7437 / σ(F): 2 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
all0.179 32530 -
obs--79.6 %
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2087
Refinement stepCycle: LAST / Resolution: 1.4→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 0 298 2087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.063
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 99 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.028

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