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- PDB-1lau: URACIL-DNA GLYCOSYLASE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1lau
TitleURACIL-DNA GLYCOSYLASE
Components
  • DNA (5'-D(*TP*TP*T)-3')
  • PROTEIN (URACIL-DNA GLYCOSYLASE (E.C.3.2.2.-))
KeywordsHYDROLASE/DNA / HYDROLASE / GLYCOSIDASE / DNA / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / host cell nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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
DNA / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsPearl, L.H. / Savva, R.
Citation
Journal: Nature / Year: 1995
Title: The structural basis of specific base-excision repair by uracil-DNA glycosylase.
Authors: Savva, R. / McAuley-Hecht, K. / Brown, T. / Pearl, L.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Analysis of the Uracil-DNA Glycosylase DNA Repair Enzyme from Herpes Simplex Virus Type 1
Authors: Savva, R. / Pearl, L.H.
History
DepositionJan 3, 1996Deposition site: BNL / Processing site: NDB
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*TP*TP*T)-3')
E: PROTEIN (URACIL-DNA GLYCOSYLASE (E.C.3.2.2.-))


Theoretical massNumber of molelcules
Total (without water)28,2342
Polymers28,2342
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.660, 61.830, 86.670
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: DNA chain DNA (5'-D(*TP*TP*T)-3')


Mass: 867.621 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (URACIL-DNA GLYCOSYLASE (E.C.3.2.2.-))


Mass: 27366.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Strain: STRAIN 17 / References: UniProt: P10186
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE URACIL-DNA GLYCOSYLASE MOLECULE IN THIS STUDY CONSISTS OF 244 AMINO ACIDS FROM THE METHIONINE ...THE URACIL-DNA GLYCOSYLASE MOLECULE IN THIS STUDY CONSISTS OF 244 AMINO ACIDS FROM THE METHIONINE AT POSITION 91 IN THE TRANSLATION OF THE UL-2 OPEN READING FRAME BEGINNING AT THE FIRST POSSIBLE START CODON. THE 90 AMINO ACIDS NOT INCLUDED IN THIS MOLECULE ARE NOT INVOLVED IN THE ACTIVITY OF THE ENZYME BUT PROBABLY CONSTITUTE A SUBCELLULAR LOCALIZATION SIGNAL. THE RESIDUES IN THIS ENTRY ARE NUMBERED RELATIVE TO THE MET 90 OF THE FULL POSSIBLE OPEN READING FRAME.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal grow
*PLUS
pH: 6.8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
154 mg/mlprotein 1drop
25.2 %PEG80001drop
334 mMammonium sulfate1drop
417 mMsodium phosphate1reservoir

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Data collection

DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 20152 / % possible obs: 90.3 % / Redundancy: 2.1 %
Reflection
*PLUS
% possible obs: 90.3 % / Redundancy: 2.1 %

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Processing

Software
NameClassification
X-PLORrefinement
MOSFLMdata reduction
RefinementResolution: 1.8→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.225 -
Rwork0.174 -
obs0.174 21482
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 61 0 161 2048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.97
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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