+Open data
-Basic information
Entry | Database: PDB / ID: 3suy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of THF riboswitch, unbound status | ||||||
Components | riboswitch | ||||||
Keywords | RNA / three-way junction / pseudoknot / gene regulator | ||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | Eubacterium siraeum V10Sc8a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å | ||||||
Authors | Huang, L. / Serganov, A. / Patel, D.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch. Authors: Huang, L. / Ishibe-Murakami, S. / Patel, D.J. / Serganov, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3suy.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3suy.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 3suy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/3suy ftp://data.pdbj.org/pub/pdb/validation_reports/su/3suy | HTTPS FTP |
---|
-Related structure data
Related structure data | 3suhC 3suxSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 32837.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA (101-MER) / Source: (synth.) Eubacterium siraeum V10Sc8a (bacteria) |
---|---|
Sequence details | THE DATABASE REFERENCE CLOSEST TO THE CRYSTALLIZED SEQUENCE IS GB 291556121 (NUCLEOTIDES RANGE: ...THE DATABASE REFERENCE CLOSEST TO THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.81 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Tris-HCl, pH 7.0 4.2 M Na-formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 7473 / Num. obs: 7451 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / Num. unique all: 738 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3SUX Resolution: 3.21→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.908 / SU B: 21.152 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.08 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.21→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.211→3.292 Å / Total num. of bins used: 20
|