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Open data
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Basic information
Entry | Database: PDB / ID: 5m48 | |||||||||||||||
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Title | Coiled coil domain of Rtt103p | |||||||||||||||
![]() | Regulator of Ty1 transposition protein 103 | |||||||||||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Jasnovidova, O. / Kalynych, S. / Plevka, P. / Stefl, R. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.4 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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.) ![]() ![]() ![]() Gene: RTT103, YDR289C / Production host: ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||
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 |
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Processing
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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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