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Open data
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Basic information
Entry | Database: PDB / ID: 5w4a | |||||||||
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Title | C. japonica N-domain | |||||||||
![]() | P-granule scaffold | |||||||||
![]() | RNA BINDING PROTEIN / P-granule scaffold protein | |||||||||
Function / homology | IMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein / : ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Aoki, S.T. / Bingman, C.A. / Kimble, J. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 535.4 KB | Display | ![]() |
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PDB format | ![]() | 451.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.1 KB | Display | ![]() |
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Full document | ![]() | 507.2 KB | Display | |
Data in XML | ![]() | 41.9 KB | Display | |
Data in CIF | ![]() | 61.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w4dSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 859 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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 |