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- PDB-1mtl: Non-productive MUG-DNA complex -

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Basic information

Entry
Database: PDB / ID: 1mtl
TitleNon-productive MUG-DNA 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 / Glycosylase / cis-platin / inter-strand / non-productive / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


double-stranded uracil-DNA glycosylase / 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: 2.8 Å
AuthorsBarrett, T.E. / Savva, R. / Barlow, T. / Brown, T. / Jiricny, J. / Pearl, L.H.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structure of a DNA base-excision product resembling a cisplatin inter-strand adduct.
Authors: Barrett, T.E. / Savva, R. / Barlow, T. / Brown, T. / Jiricny, J. / Pearl, L.H.
History
DepositionSep 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 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 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Feb 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 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,5354
Polymers44,5354
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.620, 84.860, 97.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / 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.: 2
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.: 93 / 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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 4.6
Details: PEG 4000, Ammonium sulphate, Sodium acetate, pH 4.6, Microbatch, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Ammonium sulphate11
3Sodium acetate11
Crystal grow
*PLUS
pH: 4.7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetailsSol-ID
18 %(w/v)PEG40001
2100 mMammonium sulfate1
350 mMsodium acetate1pH4.7
413 mg/mlprotein12

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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: Apr 28, 1996
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: 2.8→20 Å / Num. all: 13290 / Num. obs: 12997 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 6.5
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4 / Num. unique all: 1514 / Rsym value: 0.186 / % possible all: 96.5
Reflection
*PLUS
Num. obs: 13290 / % possible obs: 94 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native MUG structure

Resolution: 2.8→14.99 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1631387.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: RESIDUES A1, A71-A76, A165-168, B74-B77, B165-168 ARE DISORDERED RESIDUES A83, A119, B72 AND B119 WERE REFINED AS ALANINE. AAB IS AN ABASIC SITE
RfactorNum. reflection% reflectionSelection details
Rfree0.286 643 4.9 %RANDOM
Rwork0.206 ---
all0.28 13290 --
obs0.275 12997 91.9 %-
Displacement parametersBiso mean: 39.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.8→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 472 0 93 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg3.1
X-RAY DIFFRACTIONo_dihedral_angle_d23.4
X-RAY DIFFRACTIONo_improper_angle_d1.6
X-RAY DIFFRACTIONo_mcbond_it3.971.5
X-RAY DIFFRACTIONo_mcangle_it5.822
X-RAY DIFFRACTIONo_scbond_it5.762
X-RAY DIFFRACTIONo_scangle_it8.022.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 120 5.5 %
Rwork0.37 2058 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARamWATER.TOP
X-RAY DIFFRACTION3DNA2.PARamDNA2.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_angle_deg1.9
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg27.3
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg1.6

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