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Open data
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Basic information
Entry | Database: PDB / ID: 5x9v | ||||||
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Title | Crystal structure of group III chaperonin in the Closed 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 | ![]() | 368.1 KB | Display | ![]() |
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PDB format | ![]() | 298.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5x9uC ![]() 3kfeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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-ANP / #3: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.95 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.5 Details: 3 mM AMP-PNP, 20 mM MgCl2, 100 mM HEPES NaOH (pH 7.5), 22% Polyacrylic Acid 5100 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 56297 / % possible obs: 99.1 % / Redundancy: 14.9 % / Net I/σ(I): 24.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KFE Resolution: 3.003→45.152 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 24.64 / 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: 3.003→45.152 Å
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Refine LS restraints |
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LS refinement shell |
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