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Yorodumi- PDB-9bun: RhoBAST aptamer RNA in complex with 5(6)-carboxytetramethylrhodamine -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bun | |||||||||
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Title | RhoBAST aptamer RNA in complex with 5(6)-carboxytetramethylrhodamine | |||||||||
Components | RNA (48-MER) | |||||||||
Keywords | RNA / aptamer / fluorophore / dye / TAMRA | |||||||||
Function / homology | 5-carboxy methylrhodamine / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | |||||||||
Authors | Batey, R.T. / Siwik, S.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Structure of RhoBAST RNA aptamer in complex with 5(6)-carboxytetramethylrhodamine (TAMRA) Authors: Batey, R.T. / Siwik, S.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bun.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bun.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 9bun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bun_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 9bun_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 9bun_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 9bun_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/9bun ftp://data.pdbj.org/pub/pdb/validation_reports/bu/9bun | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 15586.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-IRI / #3: Chemical | ChemComp-FH8 / #4: 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: 3.22 Å3/Da / Density % sol: 61.8 % / Description: elongated prism |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 40 mM sodium cacodylate, 12 mM sodium chloride, 80 mM potassium chloride, 5% MPD, 20 mM spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0972 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 24, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0972 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→44.45 Å / Num. obs: 58528 / % possible obs: 99.9 % / Redundancy: 64.1 % / CC1/2: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.013 / Rrim(I) all: 0.103 / Χ2: 1.03 / Net I/σ(I): 34.2 / Num. measured all: 3750599 |
Reflection shell | Resolution: 1.95→2 Å / % possible obs: 99.7 % / Redundancy: 46.3 % / Rmerge(I) obs: 8.15 / Num. measured all: 188221 / Num. unique obs: 4067 / CC1/2: 0.319 / Rpim(I) all: 1.18 / Rrim(I) all: 8.239 / Χ2: 0.94 / Net I/σ(I) obs: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→44.236 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.26 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.236 Å
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Refine LS restraints |
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LS refinement shell |
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