[English] 日本語
![](img/lk-miru.gif)
- PDB-1grz: A PREORGANIZED ACTIVE SITE IN THE CRYSTAL STRUCTURE OF THE TETRAH... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1grz | ||||||
---|---|---|---|---|---|---|---|
Title | A PREORGANIZED ACTIVE SITE IN THE CRYSTAL STRUCTURE OF THE TETRAHYMENA RIBOZYME | ||||||
![]() | LSU R-RNA GROUP I INTRON | ||||||
![]() | RIBOZYME / RIBOZYME STRUCTURE / RRNA GROUP I INTRON | ||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Golden, B.L. / Gooding, A.R. / Podell, E.R. / Cech, T.R. | ||||||
![]() | ![]() Title: A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Authors: Golden, B.L. / Gooding, A.R. / Podell, E.R. / Cech, T.R. #1: ![]() Title: A strategy for crystallization of a ribozyme derived from the Tetrahymena group I intron Authors: Golden, B.L. / Podell, E.R. / Gooding, A.R. / Cech, T.R. #2: ![]() Title: Crystal structure of a group I ribozyme domain: Principles of RNA packing Authors: Cate, J.H. / Gooding, A.R. / Podell, E.R. / Zhou, K. / Golden, B.L. / Kundrot, C.E. / Cech, T.R. / Doudna, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 233.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 177.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 350.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 499.8 KB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 79896.383 Da / Num. of mol.: 2 / Fragment: RESIDUES 332-402 DELETED, LOOP 6 REPLACED BY GAGA / Mutation: U322C, U323A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5 Å3/Da / Density % sol: 75.38 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 5→25 Å / Num. all: 14377 / Num. obs: 14377 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 27 |
Reflection shell | Resolution: 5→5.18 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 10 / % possible all: 99.9 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 169 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |