[English] 日本語
Yorodumi- PDB-6i6w: Circular permutant of ribosomal protein S6, adding 6aa to C termi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i6w | ||||||
---|---|---|---|---|---|---|---|
Title | Circular permutant of ribosomal protein S6, adding 6aa to C terminal of P68-69 | ||||||
Components | 30S ribosomal protein S6,30S ribosomal protein S6 | ||||||
Keywords | RIBOSOMAL PROTEIN / Circular permutant / strand swap / local unfolding / cis-proline. / designed protein | ||||||
Function / homology | Function and homology information rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Wang, H. / Logan, D.T. / Oliveberg, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6i6w.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6i6w.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 6i6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i6w_validation.pdf.gz | 299.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6i6w_full_validation.pdf.gz | 299.9 KB | Display | |
Data in XML | 6i6w_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/6i6w ftp://data.pdbj.org/pub/pdb/validation_reports/i6/6i6w | 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 (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 11988.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: rpsF, TTHA0245 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5SLP8 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.68 % |
---|---|
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 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9801 Å | ||||||||||||||||||||||||
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
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→33.82 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.492→1.531 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|