+Open data
-Basic information
Entry | Database: PDB / ID: 5w4a | |||||||||
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Title | C. japonica N-domain | |||||||||
Components | P-granule scaffold | |||||||||
Keywords | RNA BINDING PROTEIN / P-granule scaffold protein | |||||||||
Function / homology | IMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein / : Function and homology information | |||||||||
Biological species | Caenorhabditis japonica (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Aoki, S.T. / Bingman, C.A. / Kimble, J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: C. elegans germ granules require both assembly and localized regulators for mRNA repression. Authors: Aoki, S.T. / Lynch, T.R. / Crittenden, S.L. / Bingman, C.A. / Wickens, M. / Kimble, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w4a.cif.gz | 535.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w4a.ent.gz | 451.2 KB | Display | PDB format |
PDBx/mmJSON format | 5w4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/5w4a ftp://data.pdbj.org/pub/pdb/validation_reports/w4/5w4a | HTTPS FTP |
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-Related structure data
Related structure data | 5w4dSC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24372.131 Da / Num. of mol.: 4 / Fragment: N-domain (UNP residues 1-216) Source method: isolated from a genetically manipulated source Details: codon optimized version synthesized for bacterial expression Source: (gene. exp.) Caenorhabditis japonica (invertebrata) / Plasmid: pET21a / Details (production host): IPTG inducible / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Rosetta2 / References: UniProt: H2W791, UniProt: A0A2H2IB89*PLUS |
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-Non-polymers , 6 types, 859 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PGE / #4: Chemical | ChemComp-IMD / #5: Chemical | ChemComp-PG4 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Imidazole pH 7.5, 40-45% PEG 400, 1 mM TCEP pH 7.4 PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.984 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 10, 2016 / Details: MD2 Micro Diffractometer |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30.361 Å / Num. obs: 283749 / % possible obs: 99.77 % / Redundancy: 15.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08108 / Rpim(I) all: 0.01984 / Net I/σ(I): 16.91 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.282 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 14301 / CC1/2: 0.662 / Rpim(I) all: 0.357 / % possible all: 99.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W4D Resolution: 1.5→30.361 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30.361 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -33.4193 Å / Origin y: -13.2487 Å / Origin z: 17.9092 Å
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Refinement TLS group | Selection details: all |