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- PDB-2lqz: Structure of the RNA claw of the DNA packaging motor of bacteriop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2lqz | ||||||
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Title | Structure of the RNA claw of the DNA packaging motor of bacteriophage 29 | ||||||
![]() | RNA (27-MER) | ||||||
![]() | RNA / bulge | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
![]() | Harjes, E.J. / Matsuo, H.J. / Kitamura, A.J. | ||||||
![]() | ![]() Title: Structure of the RNA claw of the DNA packaging motor of bacteriophage 29. Authors: Harjes, E. / Kitamura, A. / Zhao, W. / Morais, M.C. / Jardine, P.J. / Grimes, S. / Matsuo, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.8 KB | Display | ![]() |
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PDB format | ![]() | 127.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 558.8 KB | Display | ![]() |
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Full document | ![]() | 647.2 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: RNA chain | Mass: 8586.128 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 300 uM [U-100% 13C; U-100% 15N] RNA (27-MER), 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 300 uM / Component: RNA (27-MER)-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software | Name: CNS / Developer: Brunger A. T. et.al. / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR constraints | NA alpha-angle constraints total count: 12 / NA beta-angle constraints total count: 13 / NA chi-angle constraints total count: 12 / NA delta-angle constraints total count: 16 / NA epsilon-angle constraints total count: 12 / NA gamma-angle constraints total count: 13 / NA other-angle constraints total count: 29 / NA sugar pucker constraints total count: 99 / NOE constraints total: 429 / NOE intraresidue total count: 136 / NOE long range total count: 68 / NOE medium range total count: 33 / NOE sequential total count: 192 |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 9 |