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Yorodumi- PDB-2j5a: Folding of S6 structures with divergent amino-acid composition: p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j5a | ||||||
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Title | Folding of S6 structures with divergent amino-acid composition: pathway flexibility within partly overlapping foldons | ||||||
Components | 30S RIBOSOMAL PROTEIN S6 | ||||||
Keywords | RNA-BINDING / AQUIFEX AEOLICUS / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / RIBOSOMAL PROTEIN S6 / RRNA-BINDING / PROTEIN FOLDING | ||||||
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 | AQUIFEX AEOLICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hansson, S. / Olofsson, L. / Hedberg, L. / Oliveberg, M. / Logan, D.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Folding of S6 Structures with Divergent Amino Acid Composition: Pathway Flexibility within Partly Overlapping Foldons. Authors: Olofsson, M. / Hansson, S. / Hedberg, L. / 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 | 2j5a.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j5a.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 2j5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/2j5a ftp://data.pdbj.org/pub/pdb/validation_reports/j5/2j5a | HTTPS FTP |
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-Related structure data
Related structure data | 1g1xS S: Starting model for refinement |
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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: 13459.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66474 |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Sequence details | THE RESIDUE AT POSITION 98 HAS BEEN MODELLED AS ILE ON THE BASIS OF FIT TO ELECTRON DENSITY. THIS ...THE RESIDUE AT POSITION 98 HAS BEEN MODELLED AS ILE ON THE BASIS OF FIT TO ELECTRON DENSITY. THIS HAS NOT BEEN CONFIRMED INDEPENDEN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 62.4 % Description: BETA VERSION OF PHASER STRUCTURE SOLVED USING A PRELIMINARY 2.6A DATA SET |
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Crystal grow | Method: vapor diffusion, hanging drop Details: HANGING DROP 14% POLYETHYLENE GLYCOL 3350, 0.2M NA FORMATE, 4UL PROTEIN, 4UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→28.2 Å / Num. obs: 8252 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G1X Resolution: 2.3→25.55 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.568 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25.55 Å
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Refine LS restraints |
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