[English] 日本語
![](img/lk-miru.gif)
- PDB-1vq8: The structure of CCDA-PHE-CAP-BIO and the antibiotic sparsomycin ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1vq8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of CCDA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui | |||||||||
![]() |
| |||||||||
![]() | RIBOSOME / ribosome 50S / PROTEIN-PROTEIN COMPLEX / RNA-RNA COMPLEX / PROTEIN-RNA COMPLEX / PEPTIDYL TRANSFERASE REACTION | |||||||||
Function / homology | ![]() ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Schmeing, T.M. / Steitz, T.A. | |||||||||
![]() | ![]() Title: Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction. Authors: Schmeing, T.M. / Huang, K.S. / Kitchen, D.E. / Strobel, S.A. / Steitz, T.A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 2.5 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.9 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 313.9 KB | Display | |
Data in CIF | ![]() | 496.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vq4C ![]() 1vq5C ![]() 1vq9C ![]() 1vqkC ![]() 1vqlC ![]() 1vqmC ![]() 1vqoC ![]() 1vqpC ![]() 1s72S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-RNA chain , 3 types, 3 molecules 094
#1: RNA chain | Mass: 946090.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: RNA chain | Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: RNA chain | Mass: 1138.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CCdeoxyA-PHE-CAPROIC ACID BIOTIN OLIGOMER |
+50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules ABCDEFHJKLMNOPQRSTUVWXYZ123I
-Protein , 1 types, 1 molecules G
#10: Protein | Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Non-polymers , 8 types, 7956 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SR.gif)
![](data/chem/img/SPS.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SR.gif)
![](data/chem/img/SPS.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#33: Chemical | ChemComp-MG / #34: Chemical | #35: Chemical | ChemComp-NA / #36: Chemical | ChemComp-CL / #37: Chemical | ChemComp-SR / #38: Chemical | ChemComp-SPS / | #39: Chemical | ChemComp-CD / #40: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.02 % |
---|
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
---|---|
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 1781027 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.2→2.26 Å / Mean I/σ(I) obs: 1.2 / % possible all: 99.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 1S72 Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|