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- PDB-6i6w: Circular permutant of ribosomal protein S6, adding 6aa to C termi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i6w | ||||||
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Title | Circular permutant of ribosomal protein S6, adding 6aa to C terminal of P68-69 | ||||||
![]() | 30S ribosomal protein S6,30S ribosomal protein S6 | ||||||
![]() | RIBOSOMAL PROTEIN / Circular permutant / strand swap / local unfolding / cis-proline. / designed protein | ||||||
Function / homology | ![]() small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, H. / Logan, D.T. / Oliveberg, M. | ||||||
![]() | ![]() Title: Exposing the distinctive modular behavior of beta-strands and alpha-helices in folded proteins. Authors: Wang, H. / Logan, D.T. / Danielsson, J. / Oliveberg, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.6 KB | Display | ![]() |
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PDB format | ![]() | 41.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.4 KB | Display | ![]() |
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Full document | ![]() | 421 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i69C ![]() 6i6eC ![]() 6i6iC ![]() 6i6oC ![]() 6i6sC ![]() 6i6uC ![]() 6i6yC ![]() 1risS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11988.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.0 M Succinic acid 0.1 M HEPES pH 7.0 1% w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.49→134.03 Å / Num. obs: 14490 / % possible obs: 100 % / Redundancy: 21.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.019 / Rrim(I) all: 0.09 / Net I/σ(I): 15.5 / Num. measured all: 316130 / Scaling rejects: 7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Ris Resolution: 1.49→33.82 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.784 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.087 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 315.48 Å2 / Biso mean: 36.146 Å2 / Biso min: 22.14 Å2
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Refinement step | Cycle: final / Resolution: 1.49→33.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.492→1.531 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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