+Open data
-Basic information
Entry | Database: PDB / ID: 3bwp | ||||||
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Title | Crystal structure of a self-spliced group II intron | ||||||
Components | Group IIC intron | ||||||
Keywords | RNA / Ribonucleic acid / Intron / Group II | ||||||
Function / homology | : / : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å | ||||||
Authors | Toor, N. / Keating, K.S. / Taylor, S.D. / Pyle, A.M. | ||||||
Citation | Journal: Science / Year: 2008 Title: Crystal structure of a self-spliced group II intron Authors: Toor, N. / Keating, K.S. / Taylor, S.D. / Pyle, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bwp.cif.gz | 202.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bwp.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/3bwp ftp://data.pdbj.org/pub/pdb/validation_reports/bw/3bwp | HTTPS FTP |
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-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: 133652.156 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: sequence occurs naturally in Oceanobacillus iheyensis. Sequence modified using PCR References: GenBank: 42632302 | ||||
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#2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.5 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 6% PEG 3350, 150 mM magnesium acetate, 350 mM KCl, 50 mM Na-HEPES pH 7.0, 0.5 mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 303K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2007 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 34541 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Rmerge(I) obs: 0.149 / Χ2: 0.988 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3365 / Χ2: 1.023 / % possible all: 98.7 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.1→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: Parkinson, Vojtechovsky, Clowney, Brunger & Berman
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Displacement parameters | Biso mean: 79.413 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.21 Å
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