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Yorodumi- PDB-1q3q: Crystal structure of the chaperonin from Thermococcus strain KS-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q3q | ||||||
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Title | Crystal structure of the chaperonin from Thermococcus strain KS-1 (two-point mutant complexed with AMP-PNP) | ||||||
Components | Thermosome alpha subunit | ||||||
Keywords | CHAPERONE / chaperonin / thermosome | ||||||
Function / homology | Function and homology information chaperonin-containing T-complex / 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: 2.3 Å | ||||||
Authors | Shomura, Y. / Yoshida, T. / Iizuka, R. / Maruyama, T. / Yohda, M. / 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 | 1q3q.cif.gz | 411.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q3q.ent.gz | 334.6 KB | Display | PDB format |
PDBx/mmJSON format | 1q3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q3q_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1q3q_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1q3q_validation.xml.gz | 48 KB | Display | |
Data in CIF | 1q3q_validation.cif.gz | 72 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/1q3q ftp://data.pdbj.org/pub/pdb/validation_reports/q3/1q3q | HTTPS FTP |
-Related structure data
Related structure data | 1q2vSC 1q3rC 1q3sC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: pK1E-alpha / Plasmid: pET9a derivative / 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-MG / #3: Chemical | ChemComp-ANP / #4: 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: 3.66 Å3/Da / Density % sol: 66.43 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: ammonium sulfate, potassium chloride, Tris, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / 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: BL45XU / Wavelength: 1 Å |
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 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. all: 148110 / Num. obs: 148110 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 13.6 Å2 / Rsym value: 0.117 / Net I/σ(I): 12.4 |
Reflection shell | Highest resolution: 2.3 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.304 / % possible all: 89.7 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 590450 / Rmerge(I) obs: 0.117 |
Reflection shell | *PLUS % possible obs: 89.7 % / Rmerge(I) obs: 0.304 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q2V Resolution: 2.3→41.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 6506997.13 / Data cutoff high rms absF: 6506997.13 / 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: 35.9202 Å2 / ksol: 0.378076 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→41.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 41.9 Å / Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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