+Open data
-Basic information
Entry | Database: PDB / ID: 6ez7 | ||||||
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Title | Pes4 RRM3 Structure | ||||||
Components | Protein PES4 | ||||||
Keywords | RNA BINDING PROTEIN / RNA Recognition Motif (RRM) | ||||||
Function / homology | Function and homology information mRNA localization resulting in post-transcriptional regulation of gene expression / mRNA metabolic process / prospore membrane / poly(A) binding / poly(U) RNA binding / Translation initiation complex formation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / mRNA 3'-UTR binding ...mRNA localization resulting in post-transcriptional regulation of gene expression / mRNA metabolic process / prospore membrane / poly(A) binding / poly(U) RNA binding / Translation initiation complex formation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / ribonucleoprotein complex / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mohamad, N. / Bravo, J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: To Be Published Title: Pes4 RRM3 Structure Authors: Mohamad, N. / Bravo, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ez7.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ez7.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ez7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/6ez7 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/6ez7 | HTTPS FTP |
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-Related structure data
Related structure data | 5d77S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9763.218 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: PES4, YFR023W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39684 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | protein used to set for the crystallization plates was Pes4(303-473) however, the part that ...protein used to set for the crystallization plates was Pes4(303-473) however, the part that crystallized was Pes4(303-384) | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.08 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 200 mM Ammonium Sulfate, 30% PEG 8000, 1M MES/NaOH pH 7.4 (additive) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.212 Å / Num. obs: 10165 / % possible obs: 99.99 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.2455 / Rrim(I) all: 0.2546 / Net I/σ(I): 6.63 |
Reflection shell | Resolution: 1.9→1.94 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D77 Resolution: 1.9→29.212 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.212 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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