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Yorodumi- PDB-2gis: Structure of the S-adenosylmethionine riboswitch mRNA regulatory ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gis | ||||||
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Title | Structure of the S-adenosylmethionine riboswitch mRNA regulatory element | ||||||
Components | SAM-I riboswitch | ||||||
Keywords | RNA / mRNA / riboswitch / s-adenosylmethionine / SAM / RNA-ligand complex | ||||||
Function / homology | IRIDIUM HEXAMMINE ION / S-ADENOSYLMETHIONINE / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Montange, R.K. / Batey, R.T. | ||||||
Citation | Journal: Nature / Year: 2006 Title: Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Authors: Montange, R.K. / Batey, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gis.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gis.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 2gis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gis_validation.pdf.gz | 767.8 KB | Display | wwPDB validaton report |
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Full document | 2gis_full_validation.pdf.gz | 776.4 KB | Display | |
Data in XML | 2gis_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 2gis_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/2gis ftp://data.pdbj.org/pub/pdb/validation_reports/gi/2gis | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 30553.322 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence was engineered based on the SAM-I riboswitch from the metF-metH operon in Thermoanaerobacter tengcongensis | ||||||
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#2: Chemical | #3: Chemical | ChemComp-IRI / #4: Chemical | ChemComp-SAM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.2 % |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.10532, 1.10573 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2005 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→49.32 Å / Num. all: 15002 / Num. obs: 14940 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 14.64 % / Biso Wilson estimate: 139.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.9 | |||||||||
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 11.74 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→49.32 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 441185.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.880832 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→49.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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