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Yorodumi- PDB-1q2v: Crystal structure of the chaperonin from Thermococcus strain KS-1... -
+Open data
-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) | ||||||
Components | Thermosome alpha subunit | ||||||
Keywords | CHAPERONE / HEXADECAMER / CLOSED STATE | ||||||
Function / homology | Function and homology information ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Thermococcus sp. (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Shomura, Y. / Yoshida, T. / Iizuka, R. / Yohda, M. / Maruyama, T. / Miki, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 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: Journal: Acta Crystallogr.,Sect.D / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q2v.cif.gz | 388.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q2v.ent.gz | 319.9 KB | Display | PDB format |
PDBx/mmJSON format | 1q2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/1q2v ftp://data.pdbj.org/pub/pdb/validation_reports/q2/1q2v | HTTPS FTP |
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-Related structure data
-Links
-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). |
-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.) Thermococcus sp. (archaea) / Strain: KS-1 / Gene: THSA OR CPKA / Plasmid details: derivative of pET9a / Plasmid: pK1Ealpha / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å |
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: 0.708 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 8195547.81 / Data cutoff high rms absF: 8195547.81 / 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: 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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