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- PDB-1uug: ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WI... -

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Basic information

Entry
Database: PDB / ID: 1uug
TitleESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGI
Components
  • URACIL-DNA GLYCOSYLASE INHIBITOR
  • URACIL-DNA GLYCOSYLASE
KeywordsREPLICATION / HYDROLASE / DNA BASE EXCISION REPAIR / PROTEIN MIMICRY OF DNA / PROTEIN INHIBITOR
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
Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / 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 speciesEscherichia coli K12 (bacteria)
Bacillus phage PBS2 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMol, C.D. / Arvai, A.S. / Putnam, C.D. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase
Authors: Putnam, C.D. / Shroyer, M.J. / Lundquist, A.J. / Mol, C.D. / Arvai, A.S. / Mosbaugh, D.W. / Tainer, J.A.
History
DepositionOct 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 25, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE
B: URACIL-DNA GLYCOSYLASE INHIBITOR
C: URACIL-DNA GLYCOSYLASE
D: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)70,4164
Polymers70,4164
Non-polymers00
Water3,387188
1
A: URACIL-DNA GLYCOSYLASE
B: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)35,2082
Polymers35,2082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: URACIL-DNA GLYCOSYLASE
D: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)35,2082
Polymers35,2082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.986, 86.713, 108.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.005, 1, -0.005), (-0.999, -0.005, -0.049), (-0.049, -0.005, 0.999)-1.303, 85.908, 53.984
2given(-0.005, 1, -0.005), (-0.999, -0.005, -0.049), (-0.049, -0.005, 0.999)-1.303, 85.908, 53.984

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Components

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


Mass: 25725.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Cellular location: CYTOPLASM / Gene: UNG / Plasmid: PSB1051 / Cellular location (production host): CYTOPLASM / Gene (production host): TAC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P12295, uridine nucleosidase
#2: Protein URACIL-DNA GLYCOSYLASE INHIBITOR / UGI


Mass: 9482.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage PBS2 (virus) / Cellular location: CYTOPLASM / Plasmid: PZWTAC1 / Cellular location (production host): CYTOPLASM / Gene (production host): TAC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P14739
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growpH: 6 / Details: pH 6.0
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NACLSodium chloride11
3DIOXANE1,4-Dioxane11
4Imidazole11
5malateMalic acid11

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 29072 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.099 / Net I/σ(I): 20.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN UDG:UGI COMPLEX

Resolution: 2.4→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1336 5 %RANDOM
Rwork0.19 ---
obs-27074 97.7 %-
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.059 Å20 Å20 Å2
2---0.9 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5862 0 0 564 6426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.29
X-RAY DIFFRACTIONx_mcangle_it2.19
X-RAY DIFFRACTIONx_scbond_it2.28
X-RAY DIFFRACTIONx_scangle_it3.69
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2497 110 3 %
Rwork0.2272 1782 -
obs--51 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO

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