+
Open data
-
Basic information
Entry | Database: PDB / ID: 6qrr | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray radiation dose series on xylose isomerase - 0.13 MGy | ||||||
![]() | Xylose isomerase | ||||||
![]() | METAL BINDING PROTEIN / Isomerase | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Taberman, H. / Bury, C.S. / van der Woerd, M.J. / Snell, E.H. / Garman, E.F. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. Authors: Taberman, H. / Bury, C.S. / van der Woerd, M.J. / Snell, E.H. / Garman, E.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 219.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 173 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 37.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qrsC ![]() 6qrtC ![]() 6qruC ![]() 6qrvC ![]() 6qrwC ![]() 6qrxC ![]() 6qryC ![]() 1muwS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43195.277 Da / Num. of mol.: 1 / Mutation: E186Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 545 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-IPA / | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % |
---|---|
Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop Details: 2-propanol, ethylene glycol, HEPES, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2004 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.096→38.7 Å / Num. obs: 180192 / % possible obs: 95.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.072 / Net I/σ(I): 10.7 | |||||||||
Reflection shell | Resolution: 1.096→1.135 Å / Rrim(I) all: 0.438 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1MUW Resolution: 1.096→38.69 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.096→38.69 Å
|