+
Open data
-
Basic information
Entry | Database: PDB / ID: 2zh1 | ||||||
---|---|---|---|---|---|---|---|
Title | Complex structure of AFCCA with tRNAminiDA | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/RNA / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Nucleotidyltransferase / RNA repair / RNA-binding / tRNA processing / TRANSFERASE-RNA complex | ||||||
Function / homology | ![]() tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Toh, Y. / Tomita, K. | ||||||
![]() | ![]() Title: Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme Authors: Toh, Y. / Numata, T. / Watanabe, K. / Takeshita, D. / Nureki, O. / Tomita, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 123.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 92.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 479.8 KB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zh2C ![]() 2zh3C ![]() 2zh4C ![]() 2zh5C ![]() 2zh6C ![]() 2zh7C ![]() 2zh8C ![]() 2zh9C ![]() 2zhaC ![]() 2zhbC ![]() 2drbS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 10623.345 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
---|---|---|---|
#2: Protein | Mass: 51469.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.73 % | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 50mM HEPES, 20% PEG 3550, 0.2M Tri-lithium citrate, 80mM NH4SO4, pH 7.5, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 19808 / % possible obs: 99 % / Redundancy: 12.4 % / Biso Wilson estimate: 73.7 Å2 / Rsym value: 0.117 / Net I/σ(I): 40.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 8.5 / Num. unique all: 1957 / Rsym value: 0.453 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2DRB Resolution: 2.8→39.94 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1538350.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.189 Å2 / ksol: 0.334275 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→39.94 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|