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Open data
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Basic information
Entry | Database: PDB / ID: 5x9u | ||||||
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Title | Crystal structure of group III chaperonin in the open state | ||||||
![]() | Thermosome, alpha subunit | ||||||
![]() | CHAPERONE / group III / Archaeal-like bacterial chaperonin / closed states / pivot joints / ancestral CPN60 | ||||||
Function / homology | ![]() ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | An, Y.J. / Cha, S.S. | ||||||
![]() | ![]() Title: Structural and mechanistic characterization of an archaeal-like chaperonin from a thermophilic bacterium Authors: An, Y.J. / Rowland, S.E. / Na, J.H. / Spigolon, D. / Hong, S.K. / Yoon, Y.J. / Lee, J.H. / Robb, F.T. / Cha, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 372.4 KB | Display | ![]() |
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PDB format | ![]() | 302 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 72 KB | Display | |
Data in CIF | ![]() | 95.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x9vSC ![]() 3kfeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56689.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Z-2901 / Gene: CHY_0413 / Production host: ![]() ![]() #2: Chemical | ChemComp-ADP / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.14 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 3 mM ADP, 200 mM NH4Cl, 10mM MgCl2, 50mM HEPES sodium (pH 7.0), 5% w/v Polyethylene glycol PEG 8000, 3% 1,8-Diaminooctane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. obs: 32570 / % possible obs: 99.7 % / Redundancy: 20.3 % / Net I/σ(I): 8.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X9V,3KFE Resolution: 4.001→49.446 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.72 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.001→49.446 Å
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Refine LS restraints |
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LS refinement shell |
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