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- PDB-1p7m: SOLUTION STRUCTURE AND BASE PERTURBATION STUDIES REVEAL A NOVEL M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p7m | ||||||
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Title | SOLUTION STRUCTURE AND BASE PERTURBATION STUDIES REVEAL A NOVEL MODE OF ALKYLATED BASE RECOGNITION BY 3-METHYLADENINE DNA GLYCOSYLASE I | ||||||
![]() | DNA-3-methyladenine glycosylase I | ||||||
![]() | HYDROLASE / 3-methyladenine TAG complex nmr | ||||||
Function / homology | ![]() DNA-3-methyladenine glycosylase I / DNA-3-methyladenine glycosylase activity / base-excision repair / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
![]() | Cao, C. / Kwon, K. / Jiang, Y.L. / Drohat, A.C. / Stivers, J.T. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 377.2 KB | Display | ![]() |
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Full document | ![]() | 648.1 KB | Display | |
Data in XML | ![]() | 123.7 KB | Display | |
Data in CIF | ![]() | 155.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: Protein | Mass: 21138.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P05100, DNA-3-methyladenine glycosylase I |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-ADK / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: 1H-13C HMQC |
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Sample preparation
Details | Contents: 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 |
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Sample conditions | Ionic strength: 10mM phosphate buffer / pH: 6.6 / Pressure: ambient / Temperature: 293 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer 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 |