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- PDB-1lmz: Solution Structure of 3-Methyladenine DNA Glycosylase I (TAG) -

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Basic information

Entry
Database: PDB / ID: 1lmz
TitleSolution Structure of 3-Methyladenine DNA Glycosylase I (TAG)
Components3-methyladenine DNA glycosylase I (TAG)
KeywordsHYDROLASE / helix-hairpin-helix superfamily / DNA glycosylase / enzyme / TAG / 3-methyladenine / solution structure / NMR spectroscopy
Function / homology
Function and homology information


DNA-3-methyladenine glycosylase I / DNA-3-methyladenine glycosylase activity / base-excision repair / metal ion binding
Similarity search - Function
DNA-3-methyladenine glycosylase I / Methyladenine glycosylase / Methyladenine glycosylase / Hypothetical protein; domain 2 / DNA glycosylase / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-3-methyladenine glycosylase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Structures were calculated from an extended strand using CNS 1.1, and refined using XPLOR-NIH 1.1.2
AuthorsDrohat, A.C. / Kwon, K. / Krosky, D.J. / Stivers, J.T.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: 3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
Authors: Drohat, A.C. / Kwon, K. / Krosky, D.J. / Stivers, J.T.
History
DepositionMay 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-methyladenine DNA glycosylase I (TAG)


Theoretical massNumber of molelcules
Total (without water)21,1381
Polymers21,1381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #8lowest energy

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Components

#1: Protein 3-methyladenine DNA glycosylase I (TAG)


Mass: 21138.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Gene: TAG / Plasmid: pET21a (Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P05100, DNA-3-methyladenine glycosylase I

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1323D 15N-separated NOESY
1433D 13C-separated NOESY
1534D 13C-separated NOESY
163HNCO
173HNCA
183CBCA(CO)NH
193HN(CA)CB
1103(H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1unlabeled TAG 10 mM phosphate pH 6.6 100 mM NaCl 3 mM DTT 0.34 mM NaN3>99 % deuterium
2U-15N-labeled TAG 10 mM phosphate pH 6.6 100 mM NaCl 3 mM DTT 0.34 mM NaN393 % water, 7 % deuterium
3U-13C,15N-labled TAG 10 mM phosphate pH 6.6 100 mM NaCl 3 mM DTT 0.34 mM NaN393 % water, 7 % deuterium
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.6 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX7503
Varian UNITYPLUSVarianUNITYPLUS6004

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T.structure solution
NMRPipe2Delaglio, F.processing
Sparky3Goddard, T.D., Kneller, D.G.data analysis
XPLOR-NIH1.1.2Clore, G.M., Kuszewski, J., Schwieters, C.D., Tjandra, N.refinement
RefinementMethod: Structures were calculated from an extended strand using CNS 1.1, and refined using XPLOR-NIH 1.1.2
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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