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Yorodumi- PDB-4imi: Novel Modifications on C-terminal Domain of RNA Polymerase II can... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4imi | ||||||
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Title | Novel Modifications on C-terminal Domain of RNA Polymerase II can Fine- tune the Phosphatase Activity of Ssu72. | ||||||
Components |
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Keywords | HYDROLASE / Ssu72 / symplekin / CTD / phosphorylated Thr4 / CTD phosphatase | ||||||
Function / homology | Function and homology information Processing of Intronless Pre-mRNAs / histone locus body / Processing of Capped Intron-Containing Pre-mRNA / mRNA 3'-end processing / tricellular tight junction / RNA Polymerase II Transcription Termination / RNA polymerase II transcribes snRNA genes / Transport of Mature mRNA Derived from an Intronless Transcript / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA 3'-end processing by stem-loop binding and cleavage ...Processing of Intronless Pre-mRNAs / histone locus body / Processing of Capped Intron-Containing Pre-mRNA / mRNA 3'-end processing / tricellular tight junction / RNA Polymerase II Transcription Termination / RNA polymerase II transcribes snRNA genes / Transport of Mature mRNA Derived from an Intronless Transcript / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA 3'-end processing by stem-loop binding and cleavage / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / 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 / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) Synthetic (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Luo, Y. / Yogesha, S.D. / Zhang, Y. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Novel Modifications on C-terminal Domain of RNA Polymerase II Can Fine-tune the Phosphatase Activity of Ssu72. Authors: Luo, Y. / Yogesha, S.D. / Cannon, J.R. / Yan, W. / Ellington, A.D. / Brodbelt, J.S. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4imi.cif.gz | 211.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4imi.ent.gz | 175.4 KB | Display | PDB format |
PDBx/mmJSON format | 4imi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4imi_validation.pdf.gz | 478.6 KB | Display | wwPDB validaton report |
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Full document | 4imi_full_validation.pdf.gz | 491 KB | Display | |
Data in XML | 4imi_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 4imi_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/4imi ftp://data.pdbj.org/pub/pdb/validation_reports/im/4imi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37495.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sym, CG2097, Dmel_CG2097 / Plasmid: pET28b derivative plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8MSU4 #2: Protein | Mass: 23130.279 Da / Num. of mol.: 2 / Mutation: C13D, D144N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ssu72, CG14216, Dmel_CG14216 / Plasmid: pET28b derivative plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9VWE4, protein-serine/threonine phosphatase #3: Protein/peptide | | Mass: 2138.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in eukayotes / Source: (synth.) Synthetic (others) #4: Chemical | ChemComp-PO4 / | #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: 3.54 Å3/Da / Density % sol: 65.26 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2012 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 71363 / Num. obs: 71330 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 58.02 Å2 / Rsym value: 0.077 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3531 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→49.03 Å / Cor.coef. Fo:Fc: 0.9377 / Cor.coef. Fo:Fc free: 0.9287 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 69.02 Å2
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Refine analyze | Luzzati coordinate error obs: 0.368 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→49.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 20
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