+Open data
-Basic information
Entry | Database: PDB / ID: 4i9k | ||||||
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Title | Crystal structure of symmetric W-W-W ClpX Hexamer | ||||||
Components | ATP-dependent Clp protease ATP-binding subunit ClpX | ||||||
Keywords | MOTOR PROTEIN / ATPase / symmetric / hexamer | ||||||
Function / homology | Function and homology information protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protease binding ...protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protease binding / protein dimerization activity / cell division / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.0003 Å | ||||||
Authors | Glynn, S.E. / Nager, A.R. / Stinson, B.S. / Schmitz, K.R. / Baker, T.A. / Sauer, R.T. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2013 Title: Nucleotide Binding and Conformational Switching in the Hexameric Ring of a AAA+ Machine. Authors: Stinson, B.M. / Nager, A.R. / Glynn, S.E. / Schmitz, K.R. / Baker, T.A. / Sauer, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i9k.cif.gz | 238.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i9k.ent.gz | 193.7 KB | Display | PDB format |
PDBx/mmJSON format | 4i9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/4i9k ftp://data.pdbj.org/pub/pdb/validation_reports/i9/4i9k | HTTPS FTP |
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-Related structure data
Related structure data | 4i34C 4i4lC 4i5oC 4i63C 4i81C 3hwsS 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: 39435.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0438, clpX, JW0428, lopC / Plasmid: pACYC / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P0A6H1 #2: Chemical | ChemComp-SO4 / |
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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: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 2 M ammonium sulfate, 0.15 M potassium sulfate, 4 mM ATP, 4 mM magnesium sulfate, 50 mM EDTA, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.506→59.715 Å / Num. all: 5160 / Num. obs: 5160 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rsym value: 0.186 / Net I/σ(I): 5.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HWS Resolution: 5.0003→49.15 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5862 / SU ML: 0.75 / Phase error: 44.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 188.461 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 290.44 Å2 / Biso mean: 240.9206 Å2 / Biso min: 194.68 Å2
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Refinement step | Cycle: LAST / Resolution: 5.0003→49.15 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: 3
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