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

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Basic information

Entry
Database: PDB / ID: 1lqm
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, 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 / 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 / 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: 3.2 Å
AuthorsSaikrishnan, K. / Sagar, M.B. / Ravishankar, R. / Roy, S. / Purnapatre, K. / 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

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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
E: URACIL-DNA GLYCOSYLASE
F: URACIL-DNA GLYCOSYLASE INHIBITOR
G: URACIL-DNA GLYCOSYLASE
H: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)140,8318
Polymers140,8318
Non-polymers00
Water1,04558
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
Buried area2080 Å2
ΔGint-13 kcal/mol
Surface area13340 Å2
MethodPISA
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
Buried area2090 Å2
ΔGint-12 kcal/mol
Surface area13640 Å2
MethodPISA
3
E: URACIL-DNA GLYCOSYLASE
F: 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 area2050 Å2
ΔGint-12 kcal/mol
Surface area13620 Å2
MethodPISA
4
G: URACIL-DNA GLYCOSYLASE
H: 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 area2070 Å2
ΔGint-12 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.757, 158.875, 91.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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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.: 4
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.: 4
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.: 58 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 20mM imidazole-maleate, 10% PEG 4000, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 293K, temperature 293.0K
Crystal grow
*PLUS
Temperature: 281 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMimidazole malate1droppH7.6
310 %(w/v)PEG40001reservoir

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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: 3.2→15 Å / Num. all: 21106 / Num. obs: 21106 / % possible obs: 87.6 % / Observed criterion σ(I): 0 / Rsym value: 0.167 / Net I/σ(I): 9.2
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 1.4 / Rsym value: 0.398 / % possible all: 79.3
Reflection
*PLUS
Highest resolution: 3.2 Å / Num. measured all: 94765 / Rmerge(I) obs: 0.167
Reflection shell
*PLUS
% possible obs: 79.3 % / Rmerge(I) obs: 0.398

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Processing

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

1uug


Resolution: 3.2→15 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
Rfree0.26 916 4.9 %RANDOM
Rwork0.188 ---
obs0.188 18844 78.3 %-
all-18844 --
Displacement parametersBiso mean: 26.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-10 Å
Luzzati sigma a0.55 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9690 0 0 58 9748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_improper_angle_d0.95
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 118 4.8 %
Rwork0.254 2339 -
obs--62.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.95

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