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- PDB-1q3s: Crystal structure of the chaperonin from Thermococcus strain KS-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q3s | ||||||
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Title | Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP) | ||||||
![]() | Thermosome alpha subunit | ||||||
![]() | CHAPERONE / chaperonin / thermosome | ||||||
Function / homology | ![]() chaperonin-containing T-complex / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shomura, Y. / Yoshida, T. / Iizuka, R. / Maruyama, T. / Yohda, M. / Miki, K. | ||||||
![]() | ![]() Title: Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms. Authors: Shomura, Y. / Yoshida, T. / Iizuka, R. / Maruyama, T. / Yohda, M. / Miki, K. #1: ![]() Title: Crystallization and preliminary X-ray characterization of archaeal group II chaperonin alpha-subunit from Thermococcus strain KS-1 Authors: Shomura, Y. / Yoshida, T. / Maruyama, T. / Yohda, M. / Miki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 765.6 KB | Display | ![]() |
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PDB format | ![]() | 634 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1q2vSC ![]() 1q3qC ![]() 1q3rC 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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Details | The biological assembly is a hexadecamer generated from the octamer in the asymmetric unit by the operations: -x+1, y, -z+1/2 |
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Components
#1: Protein | Mass: 59296.586 Da / Num. of mol.: 8 / Mutation: G65C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O24729, UniProt: P61112*PLUS, EC: 3.6.4.9 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ADP / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.3 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: lithium sulfate, PEG 3350, ADA, magnesium chloride, ADP, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE |
Radiation | Monochromator: Diamond trichromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.14 Å / Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. all: 112368 / Num. obs: 112339 / % possible obs: 98 % / Redundancy: 5 % / Rsym value: 0.119 / Net I/σ(I): 13.4 |
Reflection shell | Highest resolution: 3 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.384 / % possible all: 93.7 |
Reflection | *PLUS Num. measured all: 556555 / Rmerge(I) obs: 0.119 |
Reflection shell | *PLUS % possible obs: 93.7 % / Rmerge(I) obs: 0.384 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Q2V Resolution: 3→73.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 16921226.3 / Data cutoff high rms absF: 16921226.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.6014 Å2 / ksol: 0.391713 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→73.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 73.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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