+Open data
-Basic information
Entry | Database: PDB / ID: 2n9f | ||||||
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Title | Glucose as non natural nucleobase | ||||||
Components |
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Keywords | DNA / Carbohydrate-DNA interaction / carbohydrate nucleobase | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Gomez-Pinto, I. / Vengut-Climent, E. / Lucas, R. / Avino, A. / Eritja, R. / Gonzalez-Ibanez, C. / Morales, J. / Penalver, P. / Fonseca-Guerra, C. / Bickelhaupt, M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 Title: Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA. Authors: Vengut-Climent, E. / Gomez-Pinto, I. / Lucas, R. / Penalver, P. / Avino, A. / Fonseca Guerra, C. / Bickelhaupt, F.M. / Eritja, R. / Gonzalez, C. / Morales, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n9f.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n9f.ent.gz | 127.4 KB | Display | PDB format |
PDBx/mmJSON format | 2n9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/2n9f ftp://data.pdbj.org/pub/pdb/validation_reports/n9/2n9f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3698.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using NOE data |
-Sample preparation
Details | Contents: 1 mM DNA (5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*TP*GP*AP*CP*(GL6)P*GP*CP*TP*AP*G)-3'), 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||
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Sample |
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Sample conditions | Ionic strength: Potassium phosphate / pH: 7 / Pressure: ambient / Temperature: 279.6 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 265 / NOE intraresidue total count: 131 / NOE long range total count: 16 / NOE medium range total count: 235 / NOE sequential total count: 104 | ||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10 / Conformers submitted total number: 10 |