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- PDB-1mwj: Crystal Structure of a MUG-DNA pseudo substrate complex -

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Basic information

Entry
Database: PDB / ID: 1mwj
TitleCrystal Structure of a MUG-DNA pseudo substrate complex
Components
  • 5'-D(*CP*GP*CP*GP*A*GP*(DU)P*TP*CP*GP*CP*G)-3'
  • G/U mismatch-specific DNA glycosylase
KeywordsHYDROLASE/DNA / Rossmann Fold / non-hydrolysable DNA-complex / Uracil recognition. / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


double-stranded uracil-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / uracil DNA N-glycosylase activity / DNA binding / cytoplasm
Similarity search - Function
G/U mismatch-specific DNA glycosylase MUG, bacterial / Uracil DNA glycosylase family 2 / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / G/U mismatch-specific DNA glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBarrett, T.E. / Scharer, O. / Savva, R. / Brown, T. / Jiricny, J. / Verdine, G.L. / Pearl, L.H.
CitationJournal: Embo J. / Year: 1999
Title: Crystal Structure of a thwarted mismatch glycosylase DNA repair complex
Authors: Barrett, T.E. / Scharer, O. / Savva, R. / Brown, T. / Jiricny, J. / Verdine, G.L. / Pearl, L.H.
History
DepositionSep 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). The second strand of the DNA molecule is generated by applying symmetry operator 7_555 : y, x, -z, to DU and bases 8-12, and applying symmetry operator 7_554 : y, x, -1-z, to bases 1-6.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
D: 5'-D(*CP*GP*CP*GP*A*GP*(DU)P*TP*CP*GP*CP*G)-3'
A: G/U mismatch-specific DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)22,3622
Polymers22,3622
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.996, 101.996, 45.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: DNA chain 5'-D(*CP*GP*CP*GP*A*GP*(DU)P*TP*CP*GP*CP*G)-3'


Mass: 3665.365 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein G/U mismatch-specific DNA glycosylase / MUG DNA GLYCOSYLASE / Mismatch-specific uracil DNA-glycosylase / UDG


Mass: 18696.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MUG / Plasmid: pTRC99A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P0A9H1, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 4.6
Details: PEG4000, Sodium Acetate, pH 4.6, Microbatch, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2Sodium Acetate11
3Sodium Acetate12
Crystal grow
*PLUS
Method: microdialysis / Details: Barrett, T.E., (1998) Cell., 92, 117.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaDetailsSol-ID
110 mM1MgCl2
220 mMTris-HCl1pH8.0
38 %PEG40001
40.1 Msodium acetate1pH4.62

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. all: 5478 / Num. obs: 5478 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 9.7
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2 / Num. unique all: 472 / Rsym value: 0.263 / % possible all: 85.7
Reflection
*PLUS
Num. obs: 5479 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native MuG

Resolution: 2.85→14.97 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1104323.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: NO ELECTRON DENSITY IS OBSERVED FOR RESDUES 166 TO 168 RESIDUES A1, A109, A150 AND A151 WERE REFINED AS ALANINE
RfactorNum. reflection% reflectionSelection details
Rfree0.252 237 4.5 %RANDOM
Rwork0.19 ---
all0.23 5478 --
obs0.23 5254 94.5 %-
Displacement parametersBiso mean: 22.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.85→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 243 0 58 1576
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg1.5
X-RAY DIFFRACTIONo_dihedral_angle_d24
X-RAY DIFFRACTIONo_improper_angle_d1.17
X-RAY DIFFRACTIONo_mcbond_it2.471.5
X-RAY DIFFRACTIONo_mcangle_it3.912
X-RAY DIFFRACTIONo_scbond_it4.012
X-RAY DIFFRACTIONo_scangle_it5.672.5
LS refinement shellResolution: 2.85→2.93 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.367 18 4 %
Rwork0.295 452 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARWATER.TOP
X-RAY DIFFRACTION3DNA2.PARDNA2.TOP
Software
*PLUS
Name: XPLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.23 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / Rfactor Rwork: 0.295

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