[English] 日本語
![](img/lk-miru.gif)
- PDB-8awu: Millisecond cryo-trapping by the spitrobot crystal plunger, Xylos... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8awu | ||||||
---|---|---|---|---|---|---|---|
Title | Millisecond cryo-trapping by the spitrobot crystal plunger, Xylose Isomerase with Glucose at 250ms | ||||||
![]() | Xylose isomerase | ||||||
![]() | ISOMERASE / Xylose Isomerase / Glucose Isomerase / Humidity / Space group change / Unit cell change / time-resolved crystallography | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. ...Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography. Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / ...Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 77.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8aw8C ![]() 8aw9C ![]() 8awbC ![]() 8awcC ![]() 8awdC ![]() 8aweC ![]() 8awfC ![]() 8awsC ![]() 8awvC ![]() 8awxC ![]() 8awyC ![]() 8b03C ![]() 8b05C ![]() 8b06C ![]() 8b08C ![]() 8b2oC ![]() 8b2vC ![]() 8b2wC ![]() 8b3mC ![]() 6rnfS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 43283.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Sugar | ChemComp-GLC / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-MN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % |
---|---|
Crystal grow | Temperature: 293 K / Method: batch mode Details: 35% (w/v) PEG3350, 200 mM lithium sulfate and 10 mM Hepes/NaOH pH 7.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→71.2 Å / Num. obs: 75413 / % possible obs: 99.08 % / Redundancy: 10.1 % / Biso Wilson estimate: 13.79 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.0713 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.47→1.52 Å / Num. unique obs: 6649 / CC1/2: 0.309 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6RNF Resolution: 1.47→71.2 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.61 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→71.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|