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- PDB-1udi: NUCLEOTIDE MIMICRY IN THE CRYSTAL STRUCTURE OF THE URACIL-DNA GLY... -

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Basic information

Entry
Database: PDB / ID: 1udi
TitleNUCLEOTIDE MIMICRY IN THE CRYSTAL STRUCTURE OF THE URACIL-DNA GLYCOSYLASE-URACIL GLYCOSYLASE INHIBITOR PROTEIN COMPLEX
Components
  • URACIL-DNA GLYCOSYLASE
  • URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR 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
Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / 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 ...Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / 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 / Nuclear Transport Factor 2; Chain: A, / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase / Uracil-DNA glycosylase inhibitor
Similarity search - Component
Biological speciesHerpes simplex virus
Bacillus phage PBS1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsPearl, L.H. / Savva, R.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex.
Authors: Savva, R. / Pearl, L.H.
#1: Journal: Proteins / Year: 1995
Title: Cloning and Expression of the Uracil-DNA Glycosylase Inhibitor from Bacteriophage Pbs1, and Crystallisation of a Uracil-DNA Glycosylase Uracil-DNA Glycosylase Inhibitor Complex
Authors: Savva, R. / Pearl, L.H.
#2: 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.H.
#3: 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: URACIL-DNA GLYCOSYLASE
I: URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)36,7182
Polymers36,7182
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-11 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.120, 144.120, 40.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Atom site foot note1: CIS PROLINE - PRO E 63 / 2: CIS PROLINE - PRO I 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 / Source: (natural) Herpes simplex virus (type 1 / strain 17) / Genus: Simplexvirus / Species: Human herpesvirus 1 / Strain: 17 / References: UniProt: P10186, uridine nucleosidase
#2: Protein URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN / UGI


Mass: 9351.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus phage PBS1 (virus) / References: UniProt: P14739
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal grow
*PLUS
pH: 6.8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 %(w/v)PEG800011
2100 mMsodium phosphate11
335 mMammonium sulfate11
412.5 mg/mlprotein11

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.448
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.448 Å / Relative weight: 1
ReflectionNum. obs: 12683 / % possible obs: 92.7 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.77 Å / % possible obs: 85 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2.7→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.276 -
Rwork0.188 -
obs0.188 12288
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 0 47 2519
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.863
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
Refine LS restraints
*PLUS
Type: x_improper_angle_deg / Dev ideal: 1.468

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