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Yorodumi- PDB-1dky: THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dky | ||||||
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Title | THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 2 NATIVE CRYSTALS | ||||||
Components |
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Keywords | COMPLEX (MOLECULAR CHAPERONE/PEPTIDE) / DNAK / HEAT SHOCK PROTEIN 70 KDA (HSP70) / COMPLEX (MOLECULAR CHAPERONE-PEPTIDE) / COMPLEX (MOLECULAR CHAPERONE-PEPTIDE) complex | ||||||
Function / homology | Function and homology information stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / DNA replication / ATP hydrolysis activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Zhu, X. / Zhao, X. / Burkholder, W.F. / Gragerov, A. / Ogata, C.M. / Gottesman, M.E. / Hendrickson, W.A. | ||||||
Citation | Journal: Science / Year: 1996 Title: Structural analysis of substrate binding by the molecular chaperone DnaK. Authors: Zhu, X. / Zhao, X. / Burkholder, W.F. / Gragerov, A. / Ogata, C.M. / Gottesman, M.E. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dky.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dky.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dky ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dky | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23806.750 Da / Num. of mol.: 2 / Fragment: SUBSTRATE BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6Y8 #2: Protein/peptide | Mass: 786.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #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: 2.07 Å3/Da / Density % sol: 43 % | |||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: or dialysis | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 9117 / % possible obs: 85.2 % / Observed criterion σ(I): 2 / Redundancy: 37 % |
Reflection | *PLUS Num. measured all: 23005 / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 3 Å / % possible obs: 61.6 % / Rmerge(I) obs: 0.116 |
-Processing
Software |
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Refinement | Resolution: 2.8→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 30.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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