+Open data
-Basic information
Entry | Database: PDB / ID: 1la1 | ||||||
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Title | Gro-EL Fragment (Apical Domain) Comprising Residues 188-379 | ||||||
Components | GroEL | ||||||
Keywords | CHAPERONE / MOLECULAR CHAPERONE / PROTEIN FOLDING | ||||||
Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein refolding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein refolding / response to heat / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Ashcroft, A.E. / Brinker, A. / Coyle, J.E. / Weber, F. / Kaiser, M. / Moroder, L. / Parsons, M.R. / Jager, J. / Hartl, U.F. / Hayer-Hartl, M. / Radford, S.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structural plasticity and noncovalent substrate binding in the GroEL apical domain. A study using electrospay ionization mass spectrometry and fluorescence binding studies. Authors: Ashcroft, A.E. / Brinker, A. / Coyle, J.E. / Weber, F. / Kaiser, M. / Moroder, L. / Parsons, M.R. / Jager, J. / Hartl, U.F. / Hayer-Hartl, M. / Radford, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1la1.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1la1.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 1la1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1la1_validation.pdf.gz | 370.2 KB | Display | wwPDB validaton report |
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Full document | 1la1_full_validation.pdf.gz | 376.2 KB | Display | |
Data in XML | 1la1_validation.xml.gz | 6 KB | Display | |
Data in CIF | 1la1_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/1la1 ftp://data.pdbj.org/pub/pdb/validation_reports/la/1la1 | HTTPS FTP |
-Related structure data
Related structure data | 1oelS 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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Unit cell |
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-Components
#1: Protein | Mass: 20727.852 Da / Num. of mol.: 1 / Fragment: Apical Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5 |
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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: 2.73 Å3/Da / Density % sol: 55.01 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.6 M NaCl, 14 % (w/v) PEG 6000, 100 mM Tris/HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1999 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→20 Å / Num. all: 15933 / Num. obs: 14319 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Biso Wilson estimate: 18.4 Å2 / Net I/σ(I): 10.1 |
Reflection | *PLUS Rmerge(I) obs: 0.387 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Apical domain derived from 1OEL Resolution: 2.06→19.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1242127.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber Details: CNS 1.0 followed by REFMAC was used for refinement.
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Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.06→19.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.197 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.197 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.2842 / Rfactor Rwork: 0.2491 / Rfactor obs: 0.2491 |