+Open data
-Basic information
Entry | Database: PDB / ID: 1ddy | ||||||
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Title | MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER | ||||||
Components | VITAMIN B12 BINDING RNA | ||||||
Keywords | RNA / TRIPLEX / VITAMIN B12 / APTAMER | ||||||
Function / homology | COBALAMIN / METHYLAMINE / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING / Resolution: 3 Å | ||||||
Authors | Sussman, D. / Nix, J.C. / Wilson, C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: The structural basis for molecular recognition by the vitamin B 12 RNA aptamer. Authors: Sussman, D. / Nix, J.C. / Wilson, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ddy.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ddy.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ddy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ddy_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1ddy_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 1ddy_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1ddy_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1ddy ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1ddy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: RNA chain | Mass: 11280.819 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: SEQUENCE RESULTS FROM IN VITRO SELECTION EXPERIMENTS #2: Chemical | ChemComp-B12 / #3: Chemical | ChemComp-NME / |
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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: 4.13 Å3/Da / Density % sol: 70.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: LICL, ISOPROPANOL, MGCL2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.5 / Details: Sussman, D., (1999) Acta Cryst., D55, 326. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.6047,1.6057,1.5842 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 1998 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3→20 Å / Num. all: 40156 / Num. obs: 40156 / % possible obs: 92 % / Redundancy: 3.85 % / Rsym value: 0.061 / Net I/σ(I): 13.7 | ||||||||||||
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.469 / Rsym value: 0.195 / % possible all: 80 | ||||||||||||
Reflection | *PLUS Highest resolution: 3 Å |
-Processing
Software |
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Refinement | Method to determine structure: MAD PHASING / Resolution: 3→12 Å / Rfactor Rfree error: 0.01 / Data cutoff high rms absF: 3943390.88 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Details: FOR CONSISTENCY, SUGARS PUCKERS WERE RESTRAINED TO THE A-RNA C3'-ENDO CONFORMATION. THIS MIGHT CONTRIBUTE TO THE HIGH RMSD FROM IDEAL VALUES OF IMPROPER ANGLES
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Displacement parameters | Biso mean: 26.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.18 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.248 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.322 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.283 |