+Open data
-Basic information
Entry | Database: PDB / ID: 1a6d | ||||||
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Title | THERMOSOME FROM T. ACIDOPHILUM | ||||||
Components |
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Keywords | CHAPERONIN / THERMOPLASMA ACIDOPHILUM / GROUP II CHAPERONIN / CCT / TRIC / PROTEIN FOLDING / ATPASE | ||||||
Function / homology | Function and homology information chaperonin-containing T-complex / ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å | ||||||
Authors | Ditzel, L. / Loewe, J. / Stock, D. / Stetter, K.-O. / Huber, H. / Huber, R. / Steinbacher, S. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT. Authors: Ditzel, L. / Lowe, J. / Stock, D. / Stetter, K.O. / Huber, H. / Huber, R. / Steinbacher, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a6d.cif.gz | 233.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6d.ent.gz | 188.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6d ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6d | 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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Unit cell |
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-Components
#1: Protein | Mass: 58323.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermoplasma acidophilum (acidophilic) / Cellular location: CYTOPLASM / References: UniProt: P48424 |
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#2: Protein | Mass: 58552.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermoplasma acidophilum (acidophilic) / Cellular location: CYTOPLASM / References: UniProt: P48425 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 30 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting dropDetails: 0.005ml of drop solution was mixed with 0.0025 ml of precipitant | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→15 Å / Num. obs: 42095 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.6→2.8 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.5 / % possible all: 77.3 |
Reflection shell | *PLUS % possible obs: 77.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.6→8 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 39.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.71 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3597 |