+Open data
-Basic information
Entry | Database: PDB / ID: 5da8 | ||||||
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Title | Crystal structure of chaperonin GroEL from | ||||||
Components | 60 kDa chaperonin | ||||||
Keywords | CHAPERONE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / hsp60 / chaperonin GroEL | ||||||
Function / homology | Function and homology information unfolded protein binding / protein refolding / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Chlorobium tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Chang, C. / Marshall, N. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of chaperonin GroEL from Authors: Chang, C. / Marshall, N. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5da8.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5da8.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 5da8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/5da8 ftp://data.pdbj.org/pub/pdb/validation_reports/da/5da8 | HTTPS FTP |
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-Related structure data
Related structure data | 4ki8S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58155.441 Da / Num. of mol.: 28 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria) Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / Gene: groL, groEL, CT0530 / Plasmid: pMCSG60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KF02 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MG / #5: 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: 3.02 Å3/Da / Density % sol: 59.27 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Magnesium Chloride, 0.1M Imidazole, 35% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2010 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 375234 / % possible obs: 99 % / Redundancy: 2.6 % / Biso Wilson estimate: 53.85 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.436 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KI8 Resolution: 3→48.6 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.6 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.6 Å
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Refine LS restraints |
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LS refinement shell |
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