+Open data
-Basic information
Entry | Database: PDB / ID: 5d77 | ||||||
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Title | Structure of Mip6 RRM3 Domain | ||||||
Components | RNA-binding protein MIP6 | ||||||
Keywords | RNA BINDING PROTEIN / RNA Binding Domain | ||||||
Function / homology | Function and homology information mRNA localization resulting in post-transcriptional regulation of gene expression / mRNA metabolic process / prospore membrane / sporulation / poly(A) binding / poly(U) RNA binding / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / ribonucleoprotein complex ...mRNA localization resulting in post-transcriptional regulation of gene expression / mRNA metabolic process / prospore membrane / sporulation / poly(A) binding / poly(U) RNA binding / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / ribonucleoprotein complex / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Mohamad, N. / Bravo, J. | ||||||
Citation | Journal: To Be Published Title: Structure of Mip6 RRM3 domain at 1.3 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 | 5d77.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d77.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 5d77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d77_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 5d77_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 5d77_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 5d77_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/5d77 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/5d77 | HTTPS FTP |
-Related structure data
Related structure data | 3feyS 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: 9211.569 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: MIP6, YHR015W / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus / References: UniProt: P38760 | ||||
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#2: Chemical | ChemComp-CIT / | ||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 25.12 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.5 Details: 1.6M Sodium Citrate Tribasic dihydrate pH 6.5; Ammonium Nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→45.91 Å / Num. obs: 15814 / % possible obs: 99.4 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.45 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.5 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FEY Resolution: 1.3→33.766 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→33.766 Å
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Refine LS restraints |
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LS refinement shell |
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