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Yorodumi- PDB-3p9y: Crystal structure of the Drosophila melanogaster Ssu72-pCTD complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p9y | ||||||
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Title | Crystal structure of the Drosophila melanogaster Ssu72-pCTD complex | ||||||
Components |
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Keywords | HYDROLASE / Phosphatase / cis proline / LMW PTP-like fold / RNA polymerase II CTD | ||||||
Function / homology | Function and homology information RNA polymerase II transcribes snRNA genes / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / myosin phosphatase activity / termination of RNA polymerase II transcription / protein-serine/threonine phosphatase / phosphatase activity / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Werner-Allen, J.W. / Zhou, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: cis-Proline-mediated Ser(P)5 Dephosphorylation by the RNA Polymerase II C-terminal Domain Phosphatase Ssu72. Authors: Werner-Allen, J.W. / Lee, C.J. / Liu, P. / Nicely, N.I. / Wang, S. / Greenleaf, A.L. / Zhou, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p9y.cif.gz | 320.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p9y.ent.gz | 276.8 KB | Display | PDB format |
PDBx/mmJSON format | 3p9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/3p9y ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p9y | 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 23057.209 Da / Num. of mol.: 4 / Mutation: C13D,D144N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG14216, Dmel_CG14216 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q9VWE4 #2: Protein/peptide | Mass: 858.787 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic phosphopeptide / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-IMD / #4: Chemical | ChemComp-PG4 / | #5: 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: 2.96 Å3/Da / Density % sol: 58.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22% PEG monomethyl ether 550, 100 mM imidazole pH 6.5, 150 mM DL-malic acid, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 27, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 63987 / Num. obs: 63898 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36 Å / SU ML: 0.29 / σ(F): 0.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.352 Å2 / ksol: 0.399 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1015→2.1766 Å
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