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- PDB-3cgq: X-ray structure of a pseudouridine-containing yeast spliceosomal ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cgq | ||||||
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Title | X-ray structure of a pseudouridine-containing yeast spliceosomal U2 snRNA-intron branch site duplex | ||||||
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![]() | RNA / RNA double helix / Branchpoint sequence / BPS / U2 snRNA / pseudouridine / pre-mRNA splicing | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lin, Y. / Kielkopf, C.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.5 KB | Display | ![]() |
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PDB format | ![]() | 15.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 400.9 KB | Display | ![]() |
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Full document | ![]() | 400.9 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 4.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cgpC ![]() 3cgrC ![]() 3cgsC ![]() 1i9xS ![]() 1nuvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.56 % | ||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1M ammonium sulfate, 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: ![]() |
Detector | Detector: CCD / Date: Dec 21, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 3054 / Num. obs: 3027 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.053 / Net I/σ(I): 44.1 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 6 % / Mean I/σ(I) obs: 16.5 / Rsym value: 0.108 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Combination of PDB entry 1I9X and 1NUV Resolution: 2.55→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: 15.1 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.33 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→20 Å
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Refine LS restraints |
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