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Yorodumi- PDB-4odl: Structure of SlyD from Thermus thermophilus in complex with S2 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 4odl | ||||||
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Title | Structure of SlyD from Thermus thermophilus in complex with S2 peptide | ||||||
Components |
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Keywords | ISOMERASE / CHAPERONE / FKBP domain / IF domain / peptidyl-prolyl isomerase / PPIase | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / protein refolding / structural constituent of ribosome / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.916 Å | ||||||
Authors | Quistgaard, E.M. / Low, C. / Nordlund, P. | ||||||
Citation | Journal: BMC Biol. / Year: 2016 Title: Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD. Authors: Quistgaard, E.M. / Weininger, U. / Ural-Blimke, Y. / Modig, K. / Nordlund, P. / Akke, M. / Low, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4odl.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4odl.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 4odl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/4odl ftp://data.pdbj.org/pub/pdb/validation_reports/od/4odl | HTTPS FTP |
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-Related structure data
Related structure data | 4odkC 4odmC 4odnC 4odoC 4odpC 4odqC 4odrC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17400.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA0346 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLE7, peptidylprolyl isomerase #2: Protein/peptide | Mass: 1857.227 Da / Num. of mol.: 4 / Fragment: S2 peptide (UNP residues 20-34) / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P0A7V0 #3: Chemical | #4: 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: 3.83 Å3/Da / Density % sol: 67.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.916→48.012 Å / Num. all: 14963 / Num. obs: 14963 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Biso Wilson estimate: 84.82 Å2 / Rsym value: 0.047 / Net I/σ(I): 30.68 |
Reflection shell | Resolution: 2.916→2.99 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 3.27 / Num. unique all: 1071 / Rsym value: 0.679 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.916→48.012 Å / SU ML: 0.36 / σ(F): 1.99 / Phase error: 23.68 / Stereochemistry target values: ML / Details: PDB ENTRY 3LUO
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.916→48.012 Å
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Refine LS restraints |
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LS refinement shell |
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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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