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Yorodumi- PDB-6i6e: Circular permutant of ribosomal protein S6, swap strand 1 , L10A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i6e | |||||||||
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Title | Circular permutant of ribosomal protein S6, swap strand 1 , L10A mutant | |||||||||
Components | 30S ribosomal protein S6 | |||||||||
Keywords | RIBOSOMAL PROTEIN / Circular permutant / strand swap / globling unfolding / cis-proline. / designed protein | |||||||||
Function / homology | Function and homology information small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / structural constituent of ribosome / translation Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 | 6i6e.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i6e.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 6i6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i6e_validation.pdf.gz | 421.8 KB | Display | wwPDB validaton report |
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Full document | 6i6e_full_validation.pdf.gz | 422.5 KB | Display | |
Data in XML | 6i6e_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 6i6e_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/6i6e ftp://data.pdbj.org/pub/pdb/validation_reports/i6/6i6e | HTTPS FTP |
-Related structure data
Related structure data | 6i69C 6i6iC 6i6oC 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: 12488.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Gene: rpsF, TTHA0245 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5SLP8 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.02 M Magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 22% w/v Poly (acrylic acid sodium salt) 5100 |
-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: 1.2→45.05 Å / Num. obs: 27269 / % possible obs: 100 % / Redundancy: 24.2 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.012 / Rrim(I) all: 0.061 / Net I/σ(I): 23.5 / Num. measured all: 658750 / Scaling rejects: 122 | ||||||||||||||||||||||||
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: 1.2→33.79 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 13.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.52 Å2 / Biso mean: 23.5671 Å2 / Biso min: 11.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→33.79 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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