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- PDB-1lqg: ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE COMPLEX WITH URACIL-DNA G... -

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Basic information

Entry
Database: PDB / ID: 1lqg
TitleESCHERICHIA COLI URACIL-DNA GLYCOSYLASE COMPLEX WITH URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN
Components
  • URACIL-DNA GLYCOSYLASE
  • URACIL-DNA GLYCOSYLASE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GLYCOSYLASE / INHIBITOR / DNA REPAIR / BASE EXCISION / COMPLEX (HYDROLASE-INHIBITOR) / HYDROLASE-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 / 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 superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase, active site ...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 superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / 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 (E. coli)
Bacillus phage PBS2 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSaikrishnan, K. / Sagar, M.B. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG.
Authors: Saikrishnan, K. / Bidya Sagar, M. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M.
#1: Journal: Nucleic Acids Res. / Year: 1998
Title: X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (ECUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG
Authors: Ravishankar, R. / Sagar, M.B. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M.
#2: Journal: Protein Expr.Purif. / Year: 1998
Title: Use of a coupled transcriptional system for consistent overexpression and purification of UDG-UGI complex and ugi from Escherichia coli
Authors: Roy, S. / Purnapatre, K. / Handa, P. / Boyanapalli, M. / Varshney, U.
#3: Journal: 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.N. / Lundquist, A.J. / Mol, C.D. / Arvai, A.S. / Mosbaugh, D.W. / Tainer, J.A.
History
DepositionMay 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: URACIL-DNA GLYCOSYLASE INHIBITOR
D: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)70,4164
Polymers70,4164
Non-polymers00
Water2,810156
1
A: URACIL-DNA GLYCOSYLASE
C: 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
Buried area1990 Å2
ΔGint-13 kcal/mol
Surface area13490 Å2
MethodPISA
2
B: 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
Buried area2040 Å2
ΔGint-12 kcal/mol
Surface area12870 Å2
MethodPISA
3
A: URACIL-DNA GLYCOSYLASE
C: URACIL-DNA GLYCOSYLASE INHIBITOR

B: URACIL-DNA GLYCOSYLASE
D: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)70,4164
Polymers70,4164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Buried area5760 Å2
ΔGint-39 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.164, 89.902, 141.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein URACIL-DNA GLYCOSYLASE / E.C.3.2.2.- / UDG / URACIL-DNA-GLYCOSYLASE


Mass: 25725.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P12295, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Protein URACIL-DNA GLYCOSYLASE INHIBITOR


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


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 20mM Tris-HCl, 10% PEG 1250, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMTris-HCl1droppH7.6
310 %(w/v)PEG12501reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 14803 / Num. obs: 14803 / % possible obs: 98 % / Rsym value: 0.11 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.378 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 51769 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 98.2 % / Rmerge(I) obs: 0.378

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUI

1eui


Resolution: 2.9→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 969 6.9 %RANDOM
Rwork0.183 ---
obs0.183 14095 93.6 %-
all-14095 --
Displacement parametersBiso mean: 33.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.25 Å
Luzzati d res low-10 Å
Luzzati sigma a0.44 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 0 156 4767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_improper_angle_d0.83
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 154 7 %
Rwork0.242 2052 -
obs--89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.83

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