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Yorodumi- PDB-7os7: Circular permutant of ribosomal protein S6, swap helix 2, L75A, A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7os7 | ||||||
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Title | Circular permutant of ribosomal protein S6, swap helix 2, L75A, A92K mutant | ||||||
Components | 30S ribosomal protein S6,30S ribosomal protein S6 | ||||||
Keywords | RIBOSOMAL PROTEIN / Circular permutant / native stacking / / designed amyloid fibril | ||||||
Function / homology | Function and homology information rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Wang, H. / Logan, D.T. / Oliveberg, M. | ||||||
Citation | Journal: To Be Published Title: Circular permutant of ribosomal protein S6, swap helix 2, L75A, A92K mutant Authors: Wang, H. / Logan, D.T. / Oliveberg, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7os7.cif.gz | 103.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7os7.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 7os7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7os7_validation.pdf.gz | 430.4 KB | Display | wwPDB validaton report |
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Full document | 7os7_full_validation.pdf.gz | 432.2 KB | Display | |
Data in XML | 7os7_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 7os7_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/7os7 ftp://data.pdbj.org/pub/pdb/validation_reports/os/7os7 | HTTPS FTP |
-Related structure data
Related structure data | 1risS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12727.479 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / 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: 2.24 Å3/Da / Density % sol: 44.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate dibasic 14% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97996 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97996 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→148.56 Å / Num. obs: 29194 / % possible obs: 99.7 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.024 / Rrim(I) all: 0.072 / Net I/σ(I): 15.9 / Num. measured all: 253548 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||
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: 1.65→52.11 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.33 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.42 Å2 / Biso mean: 37.531 Å2 / Biso min: 17.42 Å2
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Refinement step | Cycle: final / Resolution: 1.65→52.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.688 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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