+Open data
-Basic information
Entry | Database: PDB / ID: 8d2a | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of theophylline aptamer in complex with TAL3 | ||||||
Components | RNA (33-MER) | ||||||
Keywords | RNA / aptamer / theophylline | ||||||
Function / homology | Chem-QB3 / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Menichelli, E. / Spraggon, G. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Discovery of small molecules that target a tertiary-structured RNA. Authors: Menichelli, E. / Lam, B.J. / Wang, Y. / Wang, V.S. / Shaffer, J. / Tjhung, K.F. / Bursulaya, B. / Nguyen, T.N. / Vo, T. / Alper, P.B. / McAllister, C.S. / Jones, D.H. / Spraggon, G. / ...Authors: Menichelli, E. / Lam, B.J. / Wang, Y. / Wang, V.S. / Shaffer, J. / Tjhung, K.F. / Bursulaya, B. / Nguyen, T.N. / Vo, T. / Alper, P.B. / McAllister, C.S. / Jones, D.H. / Spraggon, G. / Michellys, P.Y. / Joslin, J. / Joyce, G.F. / Rogers, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8d2a.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8d2a.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 8d2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d2a_validation.pdf.gz | 879.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8d2a_full_validation.pdf.gz | 880.8 KB | Display | |
Data in XML | 8d2a_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 8d2a_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/8d2a ftp://data.pdbj.org/pub/pdb/validation_reports/d2/8d2a | HTTPS FTP |
-Related structure data
Related structure data | 8d28C 8d29C 8d2bC 8d5lC 8d5oC 8dk7C 1o15S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 10637.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | #5: 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: 2.43 Å3/Da / Density % sol: 49.39 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: sodium cacodylate, PEG 8000, 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→27.91 Å / Num. obs: 9761 / % possible obs: 91.52 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 8.78 |
Reflection shell | Resolution: 2.17→2.248 Å / Num. unique obs: 911 / CC1/2: 0.731 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O15 Resolution: 2.17→27.91 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.24 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.52 Å2 / Biso mean: 39.6722 Å2 / Biso min: 13.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.17→27.91 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|