+Open data
-Basic information
Entry | Database: PDB / ID: 1ons | ||||||
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Title | Crystal structure of Escherichia coli heat shock protein YedU | ||||||
Components | Chaperone protein hchA | ||||||
Keywords | CHAPERONE / heat shock protein / stress response / YedU / HSP31 / protease | ||||||
Function / homology | Function and homology information D-lactate dehydratase / response to methylglyoxal / glyoxalase III activity / thiolester hydrolase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / protein repair / guanine deglycation / protein deglycase / protein deglycase activity / RNA repair ...D-lactate dehydratase / response to methylglyoxal / glyoxalase III activity / thiolester hydrolase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / protein repair / guanine deglycation / protein deglycase / protein deglycase activity / RNA repair / Hydrolases; Acting on ester bonds; Thioester hydrolases / response to acidic pH / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / DNA repair / protein homodimerization activity / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å | ||||||
Authors | Zhao, Y. / Fox, R.O. | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: The crystal structure of Escherichia coli heat shock protein YedU reveals three potential catalytic active sites Authors: Zhao, Y. / Liu, D. / Kaluarachchi, W.D. / Bellamy, H.D. / White, M.A. / Fox, R.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ons.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ons.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ons.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ons_validation.pdf.gz | 415.2 KB | Display | wwPDB validaton report |
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Full document | 1ons_full_validation.pdf.gz | 418.2 KB | Display | |
Data in XML | 1ons_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1ons_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/1ons ftp://data.pdbj.org/pub/pdb/validation_reports/on/1ons | HTTPS FTP |
-Related structure data
Similar structure data |
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-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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Details | The second part of the biological assembly is generated by the two fold axis: x, x-y+1, -z+1/6. |
-Components
#1: Protein | Mass: 31095.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HCHA OR B1967 / Plasmid: PET30-XA-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P31658 |
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#2: Chemical | ChemComp-ZN / |
#3: 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: 2.2 Å3/Da / Density % sol: 43.6 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 600 and ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: CAMD / Beamline: GCPCC / Wavelength: 1.54 Å |
Detector | Type: MACSCIENCE / Detector: CCD / Date: Nov 12, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→90 Å / Num. all: 16033 / Num. obs: 15151 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / % possible all: 77.5 |
Reflection | *PLUS Num. measured all: 290299 |
Reflection shell | *PLUS % possible obs: 77.5 % / Num. unique obs: 779 / Rmerge(I) obs: 0.319 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.25 Å
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.203 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.2 Å |