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Yorodumi- PDB-2ydh: Crystal structure of the SAM-I riboswitch A94G U34 G18U G19U vari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ydh | ||||||
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Title | Crystal structure of the SAM-I riboswitch A94G U34 G18U G19U variant in complex with SAM | ||||||
Components | SAM-I RIBOSWITCH | ||||||
Keywords | RNA / K-TURN | ||||||
Function / homology | : / S-ADENOSYLMETHIONINE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | THERMOANAEROBACTER TENGCONGENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Schroeder, K.T. / Daldrop, P. / Lilley, D.M.J. | ||||||
Citation | Journal: Structure / Year: 2011 Title: RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn. Authors: Schroeder, K.T. / Daldrop, P. / Lilley, D.M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ydh.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ydh.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ydh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/2ydh ftp://data.pdbj.org/pub/pdb/validation_reports/yd/2ydh | HTTPS FTP |
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-Related structure data
Related structure data | 2yghC 3gx5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 30490.258 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically / Details: APTAMER DOMAIN Source: (synth.) THERMOANAEROBACTER TENGCONGENSIS (bacteria) | ||||||||
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#2: Chemical | ChemComp-BA / #3: Chemical | ChemComp-SAM / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, G 18 TO U ENGINEERED RESIDUE IN CHAIN A, G 19 TO U ENGINEERED ...ENGINEERED | Sequence details | MUTATIONS AT RESIDUES 18, 19, 34 AND 94. SEE REMARK 400 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 7 Details: 40 MM NA-CACODYLATE (PH 7.0), 12 MM SPERMINE-HCL, 12% (V/V) MPD, 80 MM KCL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 6875 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 40.6 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.44 / % possible all: 64.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GX5 Resolution: 2.9→57.62 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / ESU R Free: 0.573 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.153 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→57.62 Å
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Refine LS restraints |
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