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Yorodumi- PDB-6i6o: Circular permutant of ribosomal protein S6, swap helix 2, L75A mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i6o | ||||||
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Title | Circular permutant of ribosomal protein S6, swap helix 2, L75A mutant | ||||||
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: 1.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i6o.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i6o.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 6i6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i6o_validation.pdf.gz | 306.9 KB | Display | wwPDB validaton report |
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Full document | 6i6o_full_validation.pdf.gz | 307.4 KB | Display | |
Data in XML | 6i6o_validation.xml.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/6i6o ftp://data.pdbj.org/pub/pdb/validation_reports/i6/6i6o | HTTPS FTP |
-Related structure data
Related structure data | 6i69C 6i6eC 6i6iC 6i6sC 6i6uC 6i6wC 6i6yC 1risS 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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Unit cell |
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-Components
#1: Protein | Mass: 12425.176 Da / Num. of mol.: 4 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 / | |
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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: 2.13 Å3/Da / Density % sol: 42.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium fluoride 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→65.58 Å / Num. obs: 34312 / % possible obs: 99.9 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.027 / Rrim(I) all: 0.094 / Net I/σ(I): 15.8 / Num. measured all: 414291 / Scaling rejects: 120 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Ris Resolution: 1.9→65.58 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.397 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.15 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: 83.07 Å2 / Biso mean: 28.473 Å2 / Biso min: 12.46 Å2
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Refinement step | Cycle: final / Resolution: 1.9→65.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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