[English] 日本語

- PDB-1dky: THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1dky | ||||||
---|---|---|---|---|---|---|---|
Title | THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 2 NATIVE CRYSTALS | ||||||
![]() |
| ||||||
![]() | COMPLEX (MOLECULAR CHAPERONE/PEPTIDE) / ![]() ![]() | ||||||
Function / homology | ![]() sigma factor antagonist activity / protein-containing complex disassembly / chaperone cofactor-dependent protein refolding / cellular response to unfolded protein / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Zhu, X. / Zhao, X. / Burkholder, W.F. / Gragerov, A. / Ogata, C.M. / Gottesman, M.E. / Hendrickson, W.A. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 82.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 65.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 254 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 264.9 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | ![]() Mass: 23806.750 Da / Num. of mol.: 2 / Fragment: SUBSTRATE BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #2: Protein/peptide | Mass: 786.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 43 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: or dialysis | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.8→8 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|