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Yorodumi- PDB-1ngu: NMR Structure of Putative 3'Terminator for B. Anthracis pagA Gene... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ngu | ||||||||||||||||||||
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Title | NMR Structure of Putative 3'Terminator for B. Anthracis pagA Gene Noncoding Strand | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / B-Form DNA Hairpin | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / minimization molecular dynamics | Model type details | minimized average | Authors | Shiflett, P.R. / Taylor-McCabe, K.J. / Michalczyk, R. / Silks, L.A. / Gupta, G. | Citation | Journal: Biochemistry / Year: 2003 | Title: Structural Studies on the Hairpins at the 3' Untranslated Region of an Anthrax Toxin Gene Authors: Shiflett, P.R. / Taylor-McCabe, K.J. / Michalczyk, R. / Silks, L.A. / Gupta, G. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ngu.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ngu.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 1ngu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/1ngu ftp://data.pdbj.org/pub/pdb/validation_reports/ng/1ngu | 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: 8225.333 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs on the noncoding strand of the 3' UTR of the pagA (110) gene of Bacillus anthracis. |
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-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 standard 2D homonuclear techniques. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 150mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 278 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 | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: minimization molecular dynamics / Software ordinal: 1 Details: Structure is derived from 206 NOEs of which, 23 NOEs involvE exchangeable protons in the stem, 131 NOEs involve non-exchangeable protons in the stem, 52 NOEs involve non-exchangeable protons ...Details: Structure is derived from 206 NOEs of which, 23 NOEs involvE exchangeable protons in the stem, 131 NOEs involve non-exchangeable protons in the stem, 52 NOEs involve non-exchangeable protons in the loop, 46 Distance restraints involve hydrogen bonds, and 44 dihedral angle restraints. | ||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||
NMR ensemble | Conformer selection criteria: Submitted conformers include minimized average from molecular dynamics and 4 representative diverging structures. Conformers calculated total number: 100 / Conformers submitted total number: 5 |