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Yorodumi- PDB-1lzw: Structural basis of ClpS-mediated switch in ClpA substrate recognition -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lzw | ||||||
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Title | Structural basis of ClpS-mediated switch in ClpA substrate recognition | ||||||
Components |
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Keywords | CHAPERONE / alpha-beta-protein (ClpS) / alpha-protein (ClpA-ND) | ||||||
Function / homology | Function and homology information endopeptidase Clp complex / molecular function inhibitor activity / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / protein catabolic process / protein-folding chaperone binding / cellular response to heat / response to heat / response to oxidative stress ...endopeptidase Clp complex / molecular function inhibitor activity / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / protein catabolic process / protein-folding chaperone binding / cellular response to heat / response to heat / response to oxidative stress / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Zeth, K. / Ravelli, R.B. / Paal, K. / Cusack, S. / Bukau, B. / Dougan, D.A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA Authors: Zeth, K. / Ravelli, R.B. / Paal, K. / Cusack, S. / Bukau, B. / Dougan, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lzw.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lzw.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1lzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lzw_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 1lzw_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 1lzw_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1lzw_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/1lzw ftp://data.pdbj.org/pub/pdb/validation_reports/lz/1lzw | HTTPS FTP |
-Related structure data
-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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-Components
#1: Protein | Mass: 12125.969 Da / Num. of mol.: 1 / Mutation: H66A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q6 |
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#2: Protein | Mass: 16573.650 Da / Num. of mol.: 1 / Fragment: Residues 1-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABH9 |
#3: Chemical | ChemComp-PT / |
#4: 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: 3.49 Å3/Da / Density % sol: 64.76 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% iPr, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 278 K / pH: 7.5 / Details: Zeth, K., (2002) Acta Crystallogr., D58, 1207. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2001 / Details: mirrors |
Radiation | Monochromator: beam collimation 100 x 100 um monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.69 Å / Num. obs: 14343 / % possible obs: 98.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.122 / Net I/σ(I): 17.9 |
Reflection shell | Highest resolution: 2.5 Å / % possible all: 98.6 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 26527 / % possible obs: 98.3 % / Num. measured all: 55297 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 95.7 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.52 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→19.69 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 87059.26 / Data cutoff high rms absF: 87059.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.8347 Å2 / ksol: 0.354532 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.37 Å / Luzzati sigma a free: 0.47 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 40 Å / Num. reflection obs: 14573 / Num. reflection Rfree: 718 / % reflection Rfree: 10 % / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.241 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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