[English] 日本語
![](img/lk-miru.gif)
- PDB-1nuv: The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A r... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1nuv | ||||||
---|---|---|---|---|---|---|---|
Title | The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution | ||||||
![]() |
| ||||||
![]() | RNA / RIBOZYME / LEADZYME / LEAD-DEPENDENT CLEAVAGE / MG(H2O)6(II) / BULGED NUCLEOTIDES / HYDRATED MAGNESIUM / SR(II) / PSEUDOHELICAL PACKING / STICKY ENDS / ALTERNATE CONFORMATION / HOMOPURINE BASE PAIRS | ||||||
Function / homology | STRONTIUM ION / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wedekind, J.E. / Mckay, D.B. | ||||||
![]() | ![]() Title: Crystal structure of the leadzyme at 1.8 A resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation. Authors: Wedekind, J.E. / McKay, D.B. #1: ![]() Title: CRYSTAL STRUCTURE OF A LEAD DEPENDENT RIBOZYME REVEALING METAL BINDING SITES RELEVANT TO CATALYSIS Authors: Wedekind, J.E. / McKay, D.B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 76.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 423.8 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nujC C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 4194.598 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, REPORTED BY PAN & UHLENBECK #2: RNA chain | Mass: 3538.154 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, REPORTED BY PAN & UHLENBECK #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-SR / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow |
| ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 5, 1999 Details: 16 POLE WIGGLER, FLAT MIRROR, SI(311) BENT MONO WITH HORIZONTAL FOCUS |
Radiation | Monochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.88 Å / Num. obs: 24885 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.035 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.164 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 33.9 Å / Num. measured all: 228937 / Rmerge(I) obs: 0.035 |
Reflection shell | *PLUS Rmerge(I) obs: 0.164 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: NDB ENTRY UR0001 Resolution: 1.81→28.1 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||
Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 43.3844 Å2 / ksol: 0.314622 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 29.62 Å2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→28.1 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.81→1.88 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
| ||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 33.9 Å / % reflection Rfree: 8 % / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.21 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.268 |