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- PDB-1q2v: 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: 1q2v | ||||||
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Title | Crystal structure of the chaperonin from Thermococcus strain KS-1 (nucleotide-free form) | ||||||
![]() | Thermosome alpha subunit | ||||||
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Function / homology | ![]() ATP-dependent protein folding chaperone / unfolded protein binding / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shomura, Y. / Yoshida, T. / Iizuka, R. / Yohda, M. / Maruyama, T. / 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 | ![]() | 388.3 KB | Display | ![]() |
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PDB format | ![]() | 319.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | The biological assembly is a hexadecamer generated from the tetramer in the asymmetric unit by the operations: (-x+1, -y, z), (y+1/2, -x+1/2, z), and (-y+1/2, x-1/2, z). |
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Components
#1: Protein | Mass: 59284.531 Da / Num. of mol.: 4 / Mutation: G65C, I125T 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-SO4 / ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.97 % | |||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.1 M ammonium sulfate, 50 mM potassium chloride, pH 8.0, 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: MARRESEARCH / Detector: CCD / Date: Jun 17, 2000 |
Radiation | Monochromator: ROTATED-INCLINED FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→40 Å / Num. all: 134160 / Num. obs: 134045 / % possible obs: 99.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 39.3 Å2 / Rsym value: 0.055 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 62849 / Rsym value: 0.426 / % possible all: 98.1 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 134160 / Num. measured all: 614552 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 98.1 % / Rmerge(I) obs: 0.426 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.182 Å2 / ksol: 0.368671 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 19.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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