[English] 日本語
![](img/lk-miru.gif)
- PDB-5vjb: Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substituti... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5vjb | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa | ||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / guanidine / riboswitch / kissing loop / hairpin | Function / homology | GUANIDINE / SPERMINE / RNA / RNA (> 10) | ![]() Biological species | ![]() ![]() Method | ![]() ![]() ![]() ![]() Reiss, C.W. / Strobel, S.A. | Funding support | | ![]()
![]() ![]() Title: Structural basis for ligand binding to the guanidine-II riboswitch. Authors: Reiss, C.W. / Strobel, S.A. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 49.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 35.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 5246.047 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #2: Chemical | ChemComp-GAI / #3: Chemical | ChemComp-SPM / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.79 % |
---|---|
Crystal grow | Temperature: 296.15 K / Method: microbatch / pH: 5.6 Details: 1:1 ratio of 200uM RNA in crystallization buffer (10 mM MgCl2, 10 mM KCl, 10 mM HEPES-KOH, pH 7.5, and 40 mM guanidine) and crystallization reagent (45% MPD, 50 mM MES, pH 5.6, 4 mM NaCl, 40 ...Details: 1:1 ratio of 200uM RNA in crystallization buffer (10 mM MgCl2, 10 mM KCl, 10 mM HEPES-KOH, pH 7.5, and 40 mM guanidine) and crystallization reagent (45% MPD, 50 mM MES, pH 5.6, 4 mM NaCl, 40 mM KCl, and 12 mM spermine) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9193 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→40 Å / Num. obs: 25445 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 1.027 / Net I/σ(I): 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.46 Å2 / Biso mean: 40.534 Å2 / Biso min: 29.51 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→40 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.07→2.124 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|