+Open data
-Basic information
Entry | Database: PDB / ID: 3k62 | ||||||
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Title | Crystal structure of FBF-2/gld-1 FBEb complex | ||||||
Components |
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Keywords | RNA/RNA BINDING PROTEIN / FBF / fem-3 binding factor / PUF / RNA-binding specificity / base flipping / base stacking / RNA-RNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information sex differentiation / P granule / post-transcriptional regulation of gene expression / mRNA 3'-UTR binding / cell differentiation / negative regulation of translation / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wang, Y. / Opperman, L. / Wickens, M. / Hall, T.M.T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein. Authors: Wang, Y. / Opperman, L. / Wickens, M. / Hall, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k62.cif.gz | 192.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k62.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 3k62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/3k62 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/3k62 | HTTPS FTP |
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-Related structure data
Related structure data | 3k5qSC 3k5yC 3k5zC 3k61C 3k64C 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: 46962.004 Da / Num. of mol.: 1 / Fragment: UNP residues 164-575, RNA-binding domain Source method: isolated from a genetically manipulated source Details: A TEV cleavage site is inserted between GST and FBF-2. Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F21H12.5, fbf-2 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q09312 |
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#2: RNA chain | Mass: 2810.671 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#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: 2.75 Å3/Da / Density % sol: 55.32 % |
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Crystal grow | Temperature: 293 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 293K |
-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 / Date: Oct 4, 2007 |
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→27.8918 Å / Num. obs: 42208 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 24.688 Å2 / Rsym value: 0.083 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1970 / Rsym value: 0.807 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3K5Q Resolution: 1.9→27.8918 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→27.8918 Å
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Refine LS restraints |
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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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