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Yorodumi- PDB-2xnq: Structural insights into cis element recognition of non- polyaden... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xnq | ||||||
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Title | Structural insights into cis element recognition of non- polyadenylated RNAs by the Nab3-RRM | ||||||
Components | NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 3 | ||||||
Keywords | RNA BINDING PROTEIN / TRANSCRIPTION TERMINATION / RNA PROCESSING / RNA RECOGNITION / RRM | ||||||
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 / Processing of Capped Intron-Containing Pre-mRNA / mRNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Lunde, B.M. / Horner, M. / Meinhart, A. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: Structural Insights Into Cis Element Recognition of Non-Polyadenylated Rnas by the Nab3-Rrm. Authors: Lunde, B.M. / Horner, M. / Meinhart, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xnq.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xnq.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/2xnq ftp://data.pdbj.org/pub/pdb/validation_reports/xn/2xnq | HTTPS FTP |
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-Related structure data
Related structure data | 2xnrC 1wf2S C: citing same article (ref.) S: Starting model for refinement |
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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: 11154.556 Da / Num. of mol.: 1 / Fragment: RNA RECOGNITION MOTIF, RESIDUES 329-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P38996 |
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#2: Chemical | ChemComp-ACT / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE CONTAINS N-TERMINAL HIS-TAG AND THROMBIN CLEAVAGE SITE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.9 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 100MM SODIUM CACODYLATE BUFFER PH 6.5, 200MM SODIUM ACETATE, PEG 8000 AT 20-30 % (W/V). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.1271 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2010 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 15337 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.54 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WF2 Resolution: 1.3→33.56 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.471 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING AMINO ACIDS HAVE MULTIPLE CONFORMATIONS. ILE 350, MET 358, ASN 361, MET 388.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.788 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→33.56 Å
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Refine LS restraints |
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