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- PDB-1p7m: SOLUTION STRUCTURE AND BASE PERTURBATION STUDIES REVEAL A NOVEL M... -

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Basic information

Entry
Database: PDB / ID: 1p7m
TitleSOLUTION STRUCTURE AND BASE PERTURBATION STUDIES REVEAL A NOVEL MODE OF ALKYLATED BASE RECOGNITION BY 3-METHYLADENINE DNA GLYCOSYLASE I
ComponentsDNA-3-methyladenine glycosylase I
KeywordsHYDROLASE / 3-methyladenine TAG complex nmr
Function / homology
Function and homology information


DNA-3-methyladenine glycosylase I / DNA-3-methyladenine glycosylase activity / DNA alkylation repair / base-excision repair / metal ion binding
Similarity search - Function
DNA-3-methyladenine glycosylase I / Methyladenine glycosylase / : / Methyladenine glycosylase / Hypothetical protein; domain 2 / Endonuclease III; domain 1 / DNA glycosylase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-METHYL-3H-PURIN-6-YLAMINE / DNA-3-methyladenine glycosylase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCao, C. / Kwon, K. / Jiang, Y.L. / Drohat, A.C. / Stivers, J.T.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I
Authors: Cao, C. / Kwon, K. / Jiang, Y.L. / Drohat, A.C. / Stivers, J.T.
History
DepositionMay 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-3-methyladenine glycosylase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3533
Polymers21,1381
Non-polymers2152
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #8lowest energy

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Components

#1: Protein DNA-3-methyladenine glycosylase I


Mass: 21138.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TAG OR B3549 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): strain B
References: UniProt: P05100, DNA-3-methyladenine glycosylase I
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADK / 3-METHYL-3H-PURIN-6-YLAMINE / 3-METHYLADENINE


Mass: 149.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
2213D 15N-separated NOESY
3312D NOESY
44113C-edited HSQC
NMR detailsText: 1H-13C HMQC

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Sample preparation

DetailsContents: 0.5-1mM 13C, 15N, 75% 2H labeled3-methyladenine DNA glycosylase I, 100mM Nacl, 3mM DTT, 0.34mM NaN3, 10mM phosphate buffer, pH6.6 ~8, fold ( or 13C8 labeled) 3-methyladenine
Solvent system: H20
Sample conditionsIonic strength: 10mM phosphate buffer / pH: 6.6 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Varian UNITYPLUSVarianUNITYPLUS5003
Varian INOVAVarianINOVA6004
Bruker DMXBrukerDMX7505

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.structure solution
X-PLORNIH-2.0.2Clore, G.M., Kuszewski, J.refinement
Sparky3.93Goddard, T.D., Kneller, D.G.data analysis
NMRPipeNIHDelaglio, F.processing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 2494 restraints, 2140 are NOE-derived distance constraints, 222 dihedral angle restraints, 132 h-bond constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

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