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Yorodumi- PDB-3aq1: Open state monomer of a group II chaperonin from methanococcoides... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aq1 | ||||||
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Title | Open state monomer of a group II chaperonin from methanococcoides burtonii | ||||||
Components | Thermosome subunit | ||||||
Keywords | CHAPERONE / GROUP II CHAPERONIN / PROTEIN FOLDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanococcoides burtonii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.746 Å | ||||||
Authors | Harrop, S.J. / Pilak, O. / Siddiqui, K.S. / De Francisci, D. / Burg, D. / Williams, T.J. / Cavicchioli, R. / Curmi, P.M. | ||||||
Citation | Journal: ENVIRON.MICROBIOL. / Year: 2011 Title: Chaperonins from an Antarctic archaeon are predominantly monomeric: crystal structure of an open state monomer. Authors: Pilak, O. / Harrop, S.J. / Siddiqui, K.S. / Chong, K. / De Francisci, D. / Burg, D. / Williams, T.J. / Cavicchioli, R. / Curmi, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aq1.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aq1.ent.gz | 133.5 KB | Display | PDB format |
PDBx/mmJSON format | 3aq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/3aq1 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/3aq1 | HTTPS FTP |
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-Related structure data
Related structure data | 1a6dS S: Starting model for refinement |
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Similar 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 53930.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcoides burtonii (archaea) / Strain: DSM 6242 / Gene: Mbur_1960 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12UN6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M AMSO4, 2.5%(v/v) dioxane, 0.1M Mes/NaOh pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 21, 2008 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→21.505 Å / Num. all: 18736 / Num. obs: 18736 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A6D Resolution: 2.746→21.505 Å / SU ML: 0.42 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.286 Å2 / ksol: 0.315 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.746→21.505 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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