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Yorodumi- PDB-3qgc: Crystal structure of FBF-2 R288Y mutant in complex with gld-1 FBE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qgc | ||||||
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Title | Crystal structure of FBF-2 R288Y mutant in complex with gld-1 FBEa A7U mutant | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / FBF / FEM-3 BINDING FACTOR / PUF / RNA-BINDING SPECIFICITY / BASE STACKING / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information sex differentiation / P granule / post-transcriptional regulation of gene expression / mRNA 3'-UTR binding / negative regulation of translation / cell differentiation / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wang, Y. / Qiu, C. / Koh, Y.Y. / Opperman, L. / Gross, L. / Hall, T.M.T. / Wickens, M. | ||||||
Citation | Journal: Rna / Year: 2011 Title: Stacking interactions in PUF-RNA complexes. Authors: Koh, Y.Y. / Wang, Y. / Qiu, C. / Opperman, L. / Gross, L. / Tanaka Hall, T.M. / Wickens, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qgc.cif.gz | 192.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qgc.ent.gz | 149.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/3qgc ftp://data.pdbj.org/pub/pdb/validation_reports/qg/3qgc | HTTPS FTP |
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-Related structure data
Related structure data | 3qg9C 3qgbC 3k5yS 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: 47025.035 Da / Num. of mol.: 1 / Fragment: PUM-HD domain, rsidues 164-575 / Mutation: R288Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: fbf-2, F21H12.5 / Plasmid: pGex6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09312 |
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#2: RNA chain | Mass: 2809.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic RNA |
#3: 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: 2.74 Å3/Da / Density % sol: 55.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 MM TRIS PH 7.5, 10% POLYETHYLENE GLYCOL 8000, AND 8% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.6 Å / Num. all: 42240 / Num. obs: 42132 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Biso Wilson estimate: 24.006 Å2 / Rsym value: 0.155 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 5.6 / Num. unique all: 2087 / Rsym value: 0.55 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K5Y Resolution: 1.9→43.6 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.4451 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→43.6 Å
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Refine LS restraints |
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