+Open data
-Basic information
Entry | Database: PDB / ID: 3owi | ||||||
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Title | Crystal structure of the glycine riboswitch bound to glycine | ||||||
Components | (Domain II of glycine riboswitch) x 2 | ||||||
Keywords | RNA / Gene expression regulator / glycine riboswitch | ||||||
Function / homology | GLYCINE / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Vibrio cholerae MJ-1236 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.845 Å | ||||||
Authors | Huang, L. / Serganov, A. / Patel, D.J. | ||||||
Citation | Journal: Mol.Cell / Year: 2010 Title: Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Authors: Huang, L. / Serganov, A. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3owi.cif.gz | 208.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3owi.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 3owi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3owi_validation.pdf.gz | 432.1 KB | Display | wwPDB validaton report |
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Full document | 3owi_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 3owi_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 3owi_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/3owi ftp://data.pdbj.org/pub/pdb/validation_reports/ow/3owi | HTTPS FTP |
-Related structure data
Related structure data | 3owwC 3owzSC 3ox0C 3oxbC 3oxdC 3oxeC 3oxjC 3oxmC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 28735.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription synthesis / Source: (synth.) Vibrio cholerae MJ-1236 (bacteria) / References: GenBank: CP001485.1 | ||||||
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#2: RNA chain | Mass: 28655.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription synthesis / Source: (synth.) Vibrio cholerae MJ-1236 (bacteria) / References: GenBank: CP001485.1 | ||||||
#3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Nonpolymer details | THE ORIGINAL MG CHAIN IDS HAVE BEEN CHANGED TO THE CLOSEST POLYMER CHAIN. 100 HAS BEEN ADDED TO THE ...THE ORIGINAL MG CHAIN IDS HAVE BEEN CHANGED TO THE CLOSEST POLYMER CHAIN. 100 HAS BEEN ADDED TO THE ORIGINAL RESIDUE NUMBER | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.01 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.05 M Na-cacodylate, pH 5.1, 0.2 M KCl, 8 % (w/v) PEG8000, 80 mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2009 |
Radiation | Monochromator: SI mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.845→20 Å / Num. all: 19696 / Num. obs: 19420 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 58.2 |
Reflection shell | Resolution: 2.845→2.95 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1893 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OWZ Resolution: 2.845→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 28.429 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.738 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 76.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.845→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.845→2.917 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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