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- PDB-2uug: ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH H1... -

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Basic information

Entry
Database: PDB / ID: 2uug
TitleESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH H187D MUTANT 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: 2.6 Å
AuthorsPutnam, C.D. / Arvai, A.S. / Mol, 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: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)70,3704
Polymers70,3704
Non-polymers00
Water1,11762
1
A: URACIL-DNA GLYCOSYLASE
C: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)35,1852
Polymers35,1852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-12 kcal/mol
Surface area13330 Å2
MethodPISA, PQS
2
B: URACIL-DNA GLYCOSYLASE
D: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)35,1852
Polymers35,1852
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-11 kcal/mol
Surface area13210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.047, 86.515, 113.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9879, 0.08982, -0.12646), (-0.0922, 0.3156, 0.9444), (0.12473, 0.94463, -0.3035)49.63694, 7.20969, 21.47318
2given(-0.9879, 0.08982, -0.12646), (-0.0922, 0.3156, 0.9444), (0.12473, 0.94463, -0.3035)49.63694, 7.20969, 21.47318

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Components

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


Mass: 25702.123 Da / Num. of mol.: 2 / Mutation: H187D
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) / Gene: UGI / 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.: 62 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsENGINEERED MUTATION HIS187ASP

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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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 8.2 / Details: pH 8.2
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NACLSodium chloride11
3IMIDAZOLE11
4MALATEMalic acid11
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
145 %(w/v)PEG40001reservoir
22.5 %(w/v)sat1reservoirNaCl
3200 mMimidazole-malate1reservoir
41

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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: 2.6→40 Å / Num. obs: 17739 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 50.9 Å2 / Rsym value: 0.121 / Net I/σ(I): 13.6
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.457 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 82224 / Rmerge(I) obs: 0.121
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 1736 / Rmerge(I) obs: 0.457

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Processing

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

Resolution: 2.6→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: PHE A 77 AND PHE B 77 ARE CONSERVED RAMACHANDRAN OUTLIERS IN HUMAN, HSV AND E.COLI UDG
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1735 10 %RANDOM
Rwork0.178 ---
all-17647 --
obs-17647 99.9 %-
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.266 Å20 Å20 Å2
2--0.912 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 0 62 4893
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.52
X-RAY DIFFRACTIONx_mcangle_it2.64
X-RAY DIFFRACTIONx_scbond_it2.12
X-RAY DIFFRACTIONx_scangle_it3.41
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.323 163 10 %
Rwork0.286 1736 -
obs--86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21
X-RAY DIFFRACTIONx_mcbond_it1.52
X-RAY DIFFRACTIONx_scbond_it2.12
X-RAY DIFFRACTIONx_mcangle_it2.64
X-RAY DIFFRACTIONx_scangle_it3.41
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.323 / % reflection Rfree: 10 % / Rfactor Rwork: 0.286

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