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Yorodumi- PDB-2hop: Crystal structure of an E. coli thi-box riboswitch bound to pyrit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hop | ||||||
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Title | Crystal structure of an E. coli thi-box riboswitch bound to pyrithiamine | ||||||
Components | thi-box riboswitch | ||||||
Keywords | RNA / riboswitch | ||||||
Function / homology | Chem-218 / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Edwards, T.E. / Ferre-D'Amare, A.R. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition Authors: Edwards, T.E. / Ferre-D'Amare, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hop.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hop.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 2hop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/2hop ftp://data.pdbj.org/pub/pdb/validation_reports/ho/2hop | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: RNA chain | Mass: 26798.936 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: in vitro T7 RNA polymerase with 5'cis-hammerhead ribozyme and 5'-trans VS ribozyme | ||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-218 / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.34 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: grown: 30% PEG 2000, 0.2 M NH4Cl, 50 mM Bis-Tris pH 6.5, 15 mM CaCl2; 0.5 mM PT, 0.5 mM spermine, 100 mM KCl, 3 mM MgCl2; cryo: above with 20% sucrose; 680 x 80 x 80 um xtal., VAPOR ...Details: grown: 30% PEG 2000, 0.2 M NH4Cl, 50 mM Bis-Tris pH 6.5, 15 mM CaCl2; 0.5 mM PT, 0.5 mM spermine, 100 mM KCl, 3 mM MgCl2; cryo: above with 20% sucrose; 680 x 80 x 80 um xtal., VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 25, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→15 Å / Num. all: 3231 / Num. obs: 2978 / % possible obs: 91.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.3 / Num. unique all: 303 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 52.2 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→15 Å
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Refine LS restraints |
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