+Open data
-Basic information
Entry | Database: PDB / ID: 1yg6 | ||||||
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Title | ClpP | ||||||
Components | ATP-dependent Clp protease proteolytic subunit | ||||||
Keywords | HYDROLASE / Endopeptidase Clp / Caseinolytic protease / Protease Ti / Heat shock protein F21.5 | ||||||
Function / homology | Function and homology information HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation ...HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation / ATPase binding / response to heat / serine-type endopeptidase activity / proteolysis / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Bewley, M.C. / Graziano, V. / Griffin, K. / Flanagan, J.M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2006 Title: The asymmetry in the mature amino-terminus of ClpP facilitates a local symmetry match in ClpAP and ClpXP complexes. Authors: Bewley, M.C. / Graziano, V. / Griffin, K. / Flanagan, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yg6.cif.gz | 514.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yg6.ent.gz | 428.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yg6_validation.pdf.gz | 470 KB | Display | wwPDB validaton report |
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Full document | 1yg6_full_validation.pdf.gz | 532.2 KB | Display | |
Data in XML | 1yg6_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 1yg6_validation.cif.gz | 88.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/1yg6 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/1yg6 | HTTPS FTP |
-Related structure data
Related structure data | 1yg8C 1tysS S: Starting model for refinement C: citing same article (ref.) |
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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: 21586.863 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpP, lopP / Plasmid: pET9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)1146D / References: UniProt: P0A6G7, endopeptidase Clp #2: Chemical | ChemComp-MPD / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: mpd, mes, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Jun 6, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 247428 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 30 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: RESIDUES 20-193 1tys.PDB Resolution: 1.9→30 Å / Cross valid method: THOUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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