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Yorodumi- PDB-3cgp: X-ray structure of a pseudouridine-containing yeast spliceosomal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cgp | ||||||
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Title | X-ray structure of a pseudouridine-containing yeast spliceosomal U2 snRNA-intron branch site duplex bound to iodide ions | ||||||
Components |
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Keywords | RNA / RNA double helix / Branchpoint sequence / BPS / U2 snRNA / pseudouridine / pre-mRNA splicing | ||||||
Function / homology | IODIDE ION / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Lin, Y. / Kielkopf, C.L. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines. Authors: Lin, Y. / Kielkopf, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cgp.cif.gz | 27.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cgp.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 3cgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/3cgp ftp://data.pdbj.org/pub/pdb/validation_reports/cg/3cgp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 3867.360 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Central nucleotides of this sequence are highly conserved in yeast U2 snRNA | ||
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#2: RNA chain | Mass: 4116.518 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Central nucleotides of this sequence are highly conserved in yeast pre-mRNAs | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | #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: 2.83 Å3/Da / Density % sol: 56.52 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1M ammonium sulfate, 0.2M sodium iodide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→20 Å / Num. all: 12574 / Num. obs: 12181 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.043 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.57→1.63 Å / Redundancy: 3 % / Mean I/σ(I) obs: 9.7 / Rsym value: 0.122 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: our previously solved RNA duplex Resolution: 1.57→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21.4 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.09 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→20 Å
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Refine LS restraints |
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