[English] 日本語
![](img/lk-miru.gif)
- PDB-2bcz: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2bcz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1) | ||||||
![]() |
| ||||||
![]() | RNA / ribozyme / G8 / inosine | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Salter, J.D. / Wedekind, J.E. | ||||||
![]() | ![]() Title: Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer. Authors: Salter, J.D. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E. #1: ![]() Title: Conformational Heterogeneity at Position U37 of an All-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn Authors: Alam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / Wedekind, J.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 45.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 31.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 439.4 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zftC ![]() 1zfvC ![]() 1zfxC ![]() 2bcyC ![]() 2fgpC ![]() 2oueC ![]() 1zfr ![]() 2bb1 C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-RNA chain , 4 types, 4 molecules ABCD
#1: RNA chain | Mass: 4036.471 Da / Num. of mol.: 1 / Mutation: A1(DA) / Source method: obtained synthetically |
---|---|
#2: RNA chain | Mass: 3955.433 Da / Num. of mol.: 1 / Mutation: G8I / Source method: obtained synthetically |
#3: RNA chain | Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: RNA chain | Mass: 5991.568 Da / Num. of mol.: 1 / Mutation: U39C / Source method: obtained synthetically |
-Non-polymers , 3 types, 8 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / | ||
---|---|---|---|
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.79 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG550 MME, lithium sulfate, spermidine, cobalt hexamine, , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 83 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2005 |
Radiation | Monochromator: bent triangular asymmetric cut si(111) monochromator, RH-coated si for vertical focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9764 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44.3 Å / Num. all: 13689 / Num. obs: 13689 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.25 % / Biso Wilson estimate: 104.9 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 5.91 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.3 / % possible all: 98.7 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 1ZFR ![]() 1zfr Resolution: 2.4→44.3 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1771956.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: CNS v1.1
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 75.3413 Å2 / ksol: 0.319713 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.9 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→44.3 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.64 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 4
| |||||||||||||||||||||||||
Xplor file |
|