[English] 日本語
![](img/lk-miru.gif)
- PDB-7kzi: Intermediate state (QQQ) of near full-length DnaK alternatively f... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7kzi | ||||||
---|---|---|---|---|---|---|---|
Title | Intermediate state (QQQ) of near full-length DnaK alternatively fused with a substrate peptide | ||||||
![]() | Chaperone protein DnaK fused with substrate peptide,Chaperone protein DnaK fused with substrate peptide | ||||||
![]() | CHAPERONE / molecular chaperone / Hsp70 / protein folding | ||||||
Function / homology | ![]() unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, W. / Hendrickson, W.A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Intermediates in allosteric equilibria of DnaK-ATP interactions with substrate peptides Authors: Wang, W. / Hendrickson, W.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 468.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 387.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 44.3 KB | Display | |
Data in CIF | ![]() | 60.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kzuC ![]() 1dkzS ![]() 4jneS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 67929.469 Da / Num. of mol.: 2 / Fragment: Truncated (1-609),Truncated (1-609) / Mutation: T199A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Strain: K12, K-12 / Gene: dnaK, FAZ83_07380 Production host: ![]() ![]() References: UniProt: A0A6D2W465 |
---|
-Non-polymers , 5 types, 17 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.75 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES pH 7.5, 2.0M (NH4)2SO4, 2% PEG400, 0.15 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.82→49.75 Å / Num. obs: 48847 / % possible obs: 98.4 % / Redundancy: 36.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.024 / Rrim(I) all: 0.144 / Net I/σ(I): 18.2 / Num. measured all: 1800177 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4jne,1dkz Resolution: 2.82→49.75 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.48 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 227.96 Å2 / Biso mean: 71.5377 Å2 / Biso min: 27.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.82→49.75 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|