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Yorodumi- PDB-1dvk: CRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE SPLICING FACTOR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dvk | ||||||
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Title | CRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE SPLICING FACTOR PRP18 | ||||||
Components | PRP18 | ||||||
Keywords | RNA BINDING PROTEIN / pre-mRNA Splicing factor / Prp18 | ||||||
Function / homology | Function and homology information U2-type post-spliceosomal complex / nuclear mRNA surveillance / generation of catalytic spliceosome for second transesterification step / U5 snRNP / U4/U6 x U5 tri-snRNP complex / mRNA splicing, via spliceosome Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å | ||||||
Authors | Jiang, J. / Horowitz, D.S. / Xu, R.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Crystal structure of the functional domain of the splicing factor Prp18. Authors: Jiang, J. / Horowitz, D.S. / Xu, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dvk.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dvk.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dvk ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dvk | 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: Protein | Mass: 19625.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33411 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100mM MES 6.0, 25% PEG8000, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.09 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Oct 10, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.09 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. all: 18919 / Num. obs: 17664 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 19.59 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.097 / % possible all: 55.7 |
Reflection | *PLUS Num. measured all: 188477 |
-Processing
Software |
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Refinement | Resolution: 2.15→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.15→40 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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