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- PDB-1flz: URACIL DNA GLYCOSYLASE WITH UAAP -

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Basic information

Entry
Database: PDB / ID: 1flz
TitleURACIL DNA GLYCOSYLASE WITH UAAP
ComponentsURACIL-DNA 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 / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsWerner, R.M. / Jiang, Y.L. / Gordley, R.G. / Jagadeesh, G.J. / Ladner, J.E. / Xiao, G. / Tordova, M. / Gilliland, G.L. / Stivers, J.T.
Citation
Journal: Biochemistry / Year: 2000
Title: Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase.
Authors: Werner, R.M. / Jiang, Y.L. / Gordley, R.G. / Jagadeesh, G.J. / Ladner, J.E. / Xiao, G. / Tordova, M. / Gilliland, G.L. / Stivers, J.T.
#1: Journal: 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
DepositionAug 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: 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.classification / _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 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6622
Polymers25,5501
Non-polymers1121
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.210, 78.210, 80.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein URACIL-DNA GLYCOSYLASE / E.C.3.2.2.3 / UDG


Mass: 25549.910 Da / Num. of mol.: 1 / Mutation: Y19H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Production host: Escherichia coli (E. coli) / References: UniProt: P12295, uridine nucleosidase
#2: Chemical ChemComp-URA / URACIL


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na HEPES, 2% polyethylene glycol 400, 2.0M ammonium sulfate, 0.002M UAAp, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES1reservoir
22 %PEG4001reservoir
32.0 Mammonium sulfate1reservoir
414.9 mg/mlprotein1drop
52.4 mMdUAAp1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jun 11, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→36 Å / Num. all: 11949 / Num. obs: 11146 / % possible obs: 96 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / % possible all: 92
Reflection
*PLUS
Num. measured all: 79612

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
FRAMBOdata collection
X-GENdata scaling
RefinementResolution: 2.3→36 Å / Cross valid method: NONE /
RfactorNum. reflection
obs0.22 11146
all-11949
Refinement stepCycle: LAST / Resolution: 2.3→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 8 122 1940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg2.107
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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