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- PDB-1udh: THE STRUCTURAL BASIS OF SPECIFIC BASE EXCISION REPAIR BY URACIL-D... -

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Basic information

Entry
Database: PDB / ID: 1udh
TitleTHE STRUCTURAL BASIS OF SPECIFIC BASE EXCISION REPAIR BY URACIL-DNA GLYCOSYLASE
ComponentsURACIL-DNA GLYCOSYLASE
KeywordsHYDROLASE / DNA-N-GLYCOSIDASE
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 / 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 speciesHerpes simplex virus
MethodX-RAY DIFFRACTION / Resolution: 1.75 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
DepositionOct 30, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)27,6714
Polymers27,3661
Non-polymers3043
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.140, 65.140, 49.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Atom site foot note1: CIS PROLINE - PRO 63

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Components

#1: Protein URACIL-DNA GLYCOSYLASE


Mass: 27366.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ENCODED BY THE UL2 ORF OF HERPES SIMPLEX VIRUS TYPE 1
Source: (natural) Herpes simplex virus (type 1 / strain 17) / Genus: Simplexvirus / Species: Human herpesvirus 1 / Strain: 17 / References: UniProt: P10186, uridine nucleosidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-URA / URACIL


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
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

Diffraction sourceWavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 21944 / % possible obs: 94.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.029
Reflection
*PLUS
Highest resolution: 1.75 Å / Rmerge(I) obs: 0.029

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 1.75→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.237 -
Rwork0.191 -
obs0.191 21818
Refinement stepCycle: LAST / Resolution: 1.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 18 94 1938
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_deg1.86
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
Solvent computation
*PLUS
Displacement parameters
*PLUS

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