+Open data
-Basic information
Entry | Database: PDB / ID: 5m48 | |||||||||||||||
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Title | Coiled coil domain of Rtt103p | |||||||||||||||
Components | Regulator of Ty1 transposition protein 103 | |||||||||||||||
Keywords | TRANSCRIPTION / coiled coil / dimer | |||||||||||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain phosphoserine binding / retrotransposon silencing / mRNA 3'-end processing / RNA polymerase II transcribes snRNA genes / RNA polymerase II complex binding / site of double-strand break / chromatin / DNA binding / nucleus Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.593 Å | |||||||||||||||
Authors | Jasnovidova, O. / Kalynych, S. / Plevka, P. / Stefl, R. | |||||||||||||||
Funding support | Czech Republic, 4items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structure and dynamics of the RNAPII CTDsome with Rtt103. Authors: Jasnovidova, O. / Klumpler, T. / Kubicek, K. / Kalynych, S. / Plevka, P. / Stefl, R. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m48.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m48.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 5m48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m48_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 5m48_full_validation.pdf.gz | 423.5 KB | Display | |
Data in XML | 5m48_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 5m48_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/5m48 ftp://data.pdbj.org/pub/pdb/validation_reports/m4/5m48 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13819.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein was crystallized in 3.75M sodium formate at 20oC. Protein was labeled with seleno-methionine by feedback inhibition of the methionine biosynthesis pathway in M9 media. Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: RTT103, YDR289C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05543 |
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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 grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Purified protein was dialysed to 25mM Tris 200mM NaCl 1mM BME, pH = 8.0 (4oC) and concentrated to 6mg/ml. Protein was crystallized in 3.75M sodium formate. |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979, 0.9792, 0.9919, 0.9713 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2015 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.593→54.54 Å / Num. obs: 14200 / % possible obs: 100 % / Redundancy: 29.7 % / Net I/av σ(I): 1.7 / Net I/σ(I): 21.9 | |||||||||||||||
Reflection shell | Resolution: 2.5889→2.6814 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 2.593→48.554 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.593→48.554 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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