[English] 日本語
![](img/lk-miru.gif)
- PDB-4tzv: Co-crystals of the Ternary Complex Containing a T-box Stem I RNA,... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4tzv | ||||||
---|---|---|---|---|---|---|---|
Title | Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate post crystallization | ||||||
![]() |
| ||||||
![]() | RIBOSOMAL PROTEIN/RNA / RNA / riboswitch / tRNA / T-box / RIBOSOMAL PROTEIN-RNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, J. / Ferre-D'Amare, A.R. | ||||||
![]() | ![]() Title: Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration. Authors: Zhang, J. / Ferre-D'Amare, A.R. #1: ![]() Title: Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Authors: Zhang, J. / Ferre-D'Amare, A.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 125.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 90.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 472.7 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tzpC ![]() 4tzwC ![]() 4tzxC ![]() 4tzyC ![]() 4tzzC ![]() 4lckS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 8492.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: RNA chain | Mass: 24258.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: RNA chain | Mass: 33107.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.23 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 50 mM Bis-Tris (HCl) pH 6.5, 300 mM Li2SO4, and 20% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 6.5-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2013 |
Radiation | Monochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 5.03→46.03 Å / Num. obs: 3756 / % possible obs: 99.8 % / Redundancy: 13 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 5.03→5.2 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.828 / Mean I/σ(I) obs: 1.5 / % possible all: 98.9 |
-
Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4LCK Resolution: 5.03→46.03 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.34 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.03→46.03 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|