+Open data
-Basic information
Entry | Database: PDB / ID: 7l3r | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 23S Sarcin Ricin Loop with a 3-deazapurine A2670 | ||||||||||||||||||
Components | RNA (27-MER) | ||||||||||||||||||
Keywords | RNA / RNA modification / Ribosome | ||||||||||||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å | ||||||||||||||||||
Authors | Ennifar, E. / Renard, E. | ||||||||||||||||||
Funding support | Austria, 5items
| ||||||||||||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Impact of 3-deazapurine nucleobases on RNA properties. Authors: Bereiter, R. / Himmelstoss, M. / Renard, E. / Mairhofer, E. / Egger, M. / Breuker, K. / Kreutz, C. / Ennifar, E. / Micura, R. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7l3r.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7l3r.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 7l3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7l3r_validation.pdf.gz | 410.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7l3r_full_validation.pdf.gz | 410.5 KB | Display | |
Data in XML | 7l3r_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 7l3r_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/7l3r ftp://data.pdbj.org/pub/pdb/validation_reports/l3/7l3r | HTTPS FTP |
-Related structure data
Related structure data | 3dvzS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 8743.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3-deaza A2670-modified SRL RNA / Source: (synth.) synthetic construct (others) |
---|---|
#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.82 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 3.2 M (NH4)2SO4, 50 mM K-MOPS pH 7.0, 10 mM MgCl2, 10 mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.82656124355451 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82656124355451 Å / Relative weight: 1 |
Reflection | Resolution: 1.01→50 Å / Num. obs: 66875 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.81 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.07 |
Reflection shell | Resolution: 1.01→1.08 Å / Num. unique obs: 72259 / CC1/2: 0.809 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DVZ Resolution: 1.01→20.14 Å / SU ML: 0.1431 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.4918 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.01→20.14 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|