+Open data
-Basic information
Entry | Database: PDB / ID: 3u1l | ||||||
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Title | Structure of the mRNA splicing complex component Cwc2 | ||||||
Components | Pre-mRNA-splicing factor CWC2 | ||||||
Keywords | SPLICING / CSMP / Zinc Finger | ||||||
Function / homology | Function and homology information pre-mRNA binding / U2-type catalytic step 1 spliceosome / Prp19 complex / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / spliceosomal snRNP assembly / U6 snRNA binding / positive regulation of cell cycle / positive regulation of RNA splicing / mRNA splicing, via spliceosome ...pre-mRNA binding / U2-type catalytic step 1 spliceosome / Prp19 complex / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / spliceosomal snRNP assembly / U6 snRNA binding / positive regulation of cell cycle / positive regulation of RNA splicing / mRNA splicing, via spliceosome / cell cycle / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å | ||||||
Authors | Lu, P. / Lu, G. / Yan, C. / Wang, L. / Li, W. / Yin, P. | ||||||
Citation | Journal: Biochem.J. / Year: 2012 Title: Structure of the mRNA splicing complex component Cwc2: insights into RNA recognition Authors: Lu, P. / Lu, G. / Yan, C. / Wang, L. / Li, W. / Yin, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u1l.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u1l.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 3u1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/3u1l ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u1l | 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: Protein | Mass: 27373.102 Da / Num. of mol.: 1 / Fragment: UNP residues 1-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CWC2, NTC40, SLC3, YDL209C, D1041 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12046 |
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#2: Chemical | ChemComp-ZN / |
#3: 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: 2.49 Å3/Da / Density % sol: 50.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: pH 6.5, 21% PEG 3350, 200mM (NH4)2HCitrate, 100mM Na3Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.96393 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96393 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→40 Å / Num. all: 34338 / Num. obs: 34029 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 16.82 Å2 |
Reflection shell | Resolution: 1.64→1.7 Å / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.64→34.979 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8931 / SU ML: 0.18 / σ(F): 3.36 / Phase error: 17.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.786 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.08 Å2 / Biso mean: 24.9903 Å2 / Biso min: 8.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→34.979 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: 21.5469 Å / Origin y: 34.5122 Å / Origin z: 41.307 Å
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Refinement TLS group | Selection details: all |