+Open data
-Basic information
Entry | Database: PDB / ID: 5o1x | ||||||
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Title | Structure of Nrd1 RNA binding domain | ||||||
Components | Protein NRD1 | ||||||
Keywords | TRANSCRIPTION / Nrd1 / RRM / RNA-binding / transcription non-coding RNAs / Nrd1 complex | ||||||
Function / homology | Function and homology information transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / snRNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / : / nuclear mRNA surveillance ...transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / snRNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / : / nuclear mRNA surveillance / mRNA 3'-end processing / protein domain specific binding / mRNA binding / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Franco-Echevarria, E. / Perez-Canadillas, J.M. / Gonzalez, B. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition. Authors: Franco-Echevarria, E. / Gonzalez-Polo, N. / Zorrilla, S. / Martinez-Lumbreras, S. / Santiveri, C.M. / Campos-Olivas, R. / Sanchez, M. / Calvo, O. / Gonzalez, B. / Perez-Canadillas, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o1x.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o1x.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 5o1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/5o1x ftp://data.pdbj.org/pub/pdb/validation_reports/o1/5o1x | HTTPS FTP |
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-Related structure data
Related structure data | 5o1tC 5o1wSC 5o1yC 5o1zC 5o20C 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: 20108.586 Da / Num. of mol.: 1 / Fragment: UNP residues 290-468 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NRD1, YNL251C, N0868 / Production host: Escherichia coli (E. coli) / References: UniProt: P53617 | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-SCN / #4: 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: 2.26 Å3/Da / Density % sol: 45.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 0.2 M Potassium Thiocyanate, 23% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 8, 2015 / Details: KB focusing mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→92.45 Å / Num. obs: 23596 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.018 / Net I/σ(I): 26.82 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 6.1 / Num. measured obs: 24279 / Num. unique all: 1197 / CC1/2: 0.95 / Rpim(I) all: 0.136 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O1W Resolution: 1.6→50.57 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.684 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.902 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→50.57 Å
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Refine LS restraints |
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