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Yorodumi- PDB-8d28: Crystal structure of theophylline aptamer in complex with theophylline -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d28 | ||||||
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Title | Crystal structure of theophylline aptamer in complex with theophylline | ||||||
Components | RNA (33-MER) | ||||||
Keywords | RNA / aptamer / theophylline | ||||||
Function / homology | THEOPHYLLINE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Menichelli, E. / Spraggon, G. | ||||||
Funding support | 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d28.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d28.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 8d28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d28_validation.pdf.gz | 918 KB | Display | wwPDB validaton report |
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Full document | 8d28_full_validation.pdf.gz | 918 KB | Display | |
Data in XML | 8d28_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 8d28_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/8d28 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/8d28 | HTTPS FTP |
-Related structure data
Related structure data | 8d29C 8d2aC 8d2bC 8d5lC 8d5oC 8dk7C 1o15S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-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-MG / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→39.97 Å / Num. obs: 35223 / % possible obs: 93.76 % / Redundancy: 2.1 % / CC1/2: 0.999 / Net I/σ(I): 15.19 |
Reflection shell | Resolution: 1.42→1.47 Å / Redundancy: 2.1 % / Num. unique obs: 3451 / CC1/2: 0.886 / % possible all: 91.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O15 Resolution: 1.42→39.97 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 20.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.51 Å2 / Biso mean: 25.2168 Å2 / Biso min: 9.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.42→39.97 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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