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- PDB-1mwi: Crystal structure of a MUG-DNA product complex -

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Basic information

Entry
Database: PDB / ID: 1mwi
TitleCrystal structure of a MUG-DNA product complex
Components
  • 5'-D(*CP*GP*CP*GP*AP*GP*(AAB)P*TP*CP*GP*CP*G)-3'
  • G/U mismatch-specific DNA glycosylase
KeywordsHYDROLASE/DNA / DNA-glycosylase / nucleotide flipping / abasic site / 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: 2.35 Å
AuthorsBarrett, T.E. / Savva, R. / Panayotou, G. / Brown, T. / Barlow, T. / Jiricny, J. / Pearl, L.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions.
Authors: Barrett, T.E. / Savva, R. / Panayotou, G. / Barlow, T. / Brown, T. / Jiricny, J. / Pearl, L.H.
History
DepositionSep 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 9, 2014Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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_556 : y, x, 1-z, to D1P and bases 8-12, and applying symmetry operator 7_557 : y, x, 2-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*AP*GP*(AAB)P*TP*CP*GP*CP*G)-3'
A: G/U mismatch-specific DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)22,2682
Polymers22,2682
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.350, 101.350, 45.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsOne asymmetric unit consists of a single protein molecule and 1 strand of DNA. The second strand is generated by x,y,-z (translation 0,0,1) applied to APR,THY,CYT,GUA, CYT,GUA and x,y,-z (translation 0,0,2) applied to the remaining nucleic acids.

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Components

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


Mass: 3571.293 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 / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 4.6
Details: PEG 4000, Sodium acetate,, pH 4.6, Microbatch, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Sodium acetate11
3Sodium acetate12

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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: Aug 15, 1997
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: 2.35→20 Å / Num. obs: 10144 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 15
Reflection shellResolution: 2.35→2.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.2 / Rsym value: 0.2 / % possible all: 95.2

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Processing

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

Resolution: 2.35→14.93 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1604690.93 / 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. D1P CORRESPONDS TO AN ABASIC SITE
RfactorNum. reflection% reflectionSelection details
Rfree0.28 477 4.8 %RANDOM
Rwork0.21 ---
all0.2482 10144 --
obs0.2482 9878 99.2 %-
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.35→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 236 0 122 1629
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_mcbond_it1.621.5
X-RAY DIFFRACTIONx_mcangle_it2.532
X-RAY DIFFRACTIONx_scbond_it3.52
X-RAY DIFFRACTIONx_scangle_it4.82.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.29 64 5.3 %
Rwork0.28 1102 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARWATER.TOP
X-RAY DIFFRACTION3DNA2.PARDNA2.TOP

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