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Yorodumi- PDB-5mdt: Structure of the CTD-interacting domain (CID) of Seb1 from S. pombe. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mdt | ||||||||||||
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Title | Structure of the CTD-interacting domain (CID) of Seb1 from S. pombe. | ||||||||||||
Components | Rpb7-binding protein seb1 | ||||||||||||
Keywords | TRANSCRIPTION / CTD-interacting domain (CID) / S. pombe / transcription termination / RNA polymerase II | ||||||||||||
Function / homology | Function and homology information Mei2 nuclear dot complex / sno(s)RNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / regulatory ncRNA 3'-end processing / mRNA 3'-end processing / lncRNA binding / RNA polymerase II C-terminal domain binding / RNA binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||||||||
Authors | Wittmann, S. / Renner, M. / Vasiljeva, L. / Grimes, J. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Nat Commun / Year: 2017 Title: The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA. Authors: Wittmann, S. / Renner, M. / Watts, B.R. / Adams, O. / Huseyin, M. / Baejen, C. / El Omari, K. / Kilchert, C. / Heo, D.H. / Kecman, T. / Cramer, P. / Grimes, J.M. / Vasiljeva, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mdt.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mdt.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 5mdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/5mdt ftp://data.pdbj.org/pub/pdb/validation_reports/md/5mdt | HTTPS FTP |
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-Related structure data
Related structure data | 5mduC 3cljS 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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Unit cell |
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-Components
#1: Protein | Mass: 17911.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast) Gene: seb1, SPAC222.09 / Plasmid: pET41a(+) / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: Q9UTE3 |
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#2: 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: 3.26 Å3/Da / Density % sol: 62.31 % |
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Crystal grow | Temperature: 293.65 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris, 4 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2014 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→48.12 Å / Num. obs: 30490 / % possible obs: 99.3 % / Redundancy: 8.5 % / Biso Wilson estimate: 32.93 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.62→1.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 2.151 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.5 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3clj Resolution: 1.62→48.12 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9407 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.075 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.07
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Displacement parameters | Biso mean: 52.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.62→48.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.68 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: -11.4115 Å / Origin y: -17.8075 Å / Origin z: 274.823 Å
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Refinement TLS group | Selection details: { A|* } |