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Yorodumi- PDB-4pn1: Structure of S. pombe Pct1 RNA triphosphatase in complex with the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pn1 | ||||||
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Title | Structure of S. pombe Pct1 RNA triphosphatase in complex with the Spt5 CTD | ||||||
Components |
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Keywords | HYDROLASE/TRANSCRIPTION REGULATOR / mRNA triphosphatase / hydrolase / polynucleotide 5' triphosphatase / mRNA processing / mRNA capping / dimer / transcription elongation factor / HYDROLASE-TRANSCRIPTION REGULATOR complex | ||||||
Function / homology | Function and homology information 7-methylguanosine RNA capping / polynucleotide 5' dephosphorylation / mRNA capping enzyme complex / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / RNA polymerase II C-terminal domain binding / 7-methylguanosine mRNA capping / ATP hydrolysis activity / nucleus Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å | ||||||
Authors | Lima, C.D. / Doamekpor, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Rna / Year: 2015 Title: Fission yeast RNA triphosphatase reads an Spt5 CTD code. Authors: Doamekpor, S.K. / Schwer, B. / Sanchez, A.M. / Shuman, S. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pn1.cif.gz | 227.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pn1.ent.gz | 183.5 KB | Display | PDB format |
PDBx/mmJSON format | 4pn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pn1_validation.pdf.gz | 493.9 KB | Display | wwPDB validaton report |
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Full document | 4pn1_full_validation.pdf.gz | 502.7 KB | Display | |
Data in XML | 4pn1_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 4pn1_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/4pn1 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/4pn1 | HTTPS FTP |
-Related structure data
Related structure data | 4pn0SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 35586.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: pct1 / Plasmid: pSMT3 / Details (production host): his-tagged SUMO fusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): codon plus RIL / References: UniProt: Q9P6Q6, polynucleotide 5'-phosphatase #2: Protein/peptide | Mass: 1906.022 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: synthetic peptide derived from the repeating sequence found at the C-terminal domain of Spt5 #3: Chemical | ChemComp-FMT / #4: Chemical | #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: 3.02 Å3/Da / Density % sol: 59.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 3.0 M sodium formate cryo-protected in 3.2 M sodium formate and 20% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 49568 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 97.7 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PN0 Resolution: 2.803→48.362 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 23.79 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.803→48.362 Å
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Refine LS restraints |
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LS refinement shell |
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