+Open data
-Basic information
Entry | Database: PDB / ID: 5w4d | ||||||
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Title | C. japonica N-domain, Selenomethionine mutant | ||||||
Components | P-granule scaffold protein | ||||||
Keywords | RNA BINDING PROTEIN / P-granule scaffold protein | ||||||
Function / homology | IMIDAZOLE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / TRIETHYLENE GLYCOL / Uncharacterized protein / : Function and homology information | ||||||
Biological species | Caenorhabditis japonica (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.599 Å | ||||||
Authors | Aoki, S.T. / Bingman, C.A. / Kimble, J. | ||||||
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 | 5w4d.cif.gz | 524.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w4d.ent.gz | 443.2 KB | Display | PDB format |
PDBx/mmJSON format | 5w4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/5w4d ftp://data.pdbj.org/pub/pdb/validation_reports/w4/5w4d | HTTPS FTP |
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-Related 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: 24501.994 Da / Num. of mol.: 4 / Fragment: N-domain (UNP residues 1-216) / Mutation: I63M, I212M Source method: isolated from a genetically manipulated source Details: codon optimized version / Source: (gene. exp.) Caenorhabditis japonica (invertebrata) / Tissue: germline / 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 , 8 types, 680 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-IMD / #8: Chemical | ChemComp-PG5 / | #9: 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: 2.34 Å3/Da / Density % sol: 47.35 % |
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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-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2016 / Details: MD2 Micro Diffractometer |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→48.466 Å / Num. obs: 227476 / % possible obs: 97.06 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0469 / Rpim(I) all: 0.01827 / Net I/σ(I): 24.44 |
Reflection shell | Resolution: 1.599→1.656 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.8775 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 11239 / CC1/2: 0.74 / Rpim(I) all: 0.348 / % possible all: 95.16 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.599→48.466 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.599→48.466 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: -33.8159 Å / Origin y: -13.2379 Å / Origin z: 17.9354 Å
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Refinement TLS group | Selection details: all |