[English] 日本語
Yorodumi- PDB-2ygh: SAM-I riboswitch with a G2nA mutation in the Kink turn in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ygh | ||||||
---|---|---|---|---|---|---|---|
Title | SAM-I riboswitch with a G2nA mutation in the Kink turn in complex with S-adenosylmethionine | ||||||
Components | SAM-I RIBOSWITCH | ||||||
Keywords | RNA | ||||||
Function / homology | : / S-ADENOSYLMETHIONINE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | THERMOANAEROBACTER TENGCONGENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Schroeder, K. / Daldrop, P. / Lilley, D. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ygh.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ygh.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 2ygh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ygh_validation.pdf.gz | 762.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ygh_full_validation.pdf.gz | 766.6 KB | Display | |
Data in XML | 2ygh_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 2ygh_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2ygh ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2ygh | HTTPS FTP |
-Related structure data
Related structure data | 2ydhC 3gx5S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 30881.543 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) THERMOANAEROBACTER TENGCONGENSIS (bacteria) | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-SAM / | ||||||
#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | Sequence details | APTAMER DOMAIN FRAGMENT WITH MUTATION [G19A,A94G]. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 46 % / Description: NONE |
---|---|
Crystal grow | pH: 7 Details: 10 MM MGCL, 40 MM NA-CACODYLATE PH 7, 80 MM KCL, 16 MM SPERMINE-HCL, 14% (V/V) MPD. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.974 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.974 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→51.8 Å / Num. obs: 8929 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GX5 Resolution: 2.6→54.71 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.018 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.333 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→54.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|