[English] 日本語
![](img/lk-miru.gif)
- PDB-6ll2: Crystal structure of glucose isomerase by fixed-target serial fem... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ll2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of glucose isomerase by fixed-target serial femtosecond crystallography | ||||||
![]() | Xylose isomerase | ||||||
![]() | ISOMERASE / glucose isomerase / serial crystallography / sfx | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Nam, K.H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structure of glucose isomerase by fixed-target serial femtosecond crystallography Authors: Nam, K.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 100.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.4 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zyeS S: Starting model for refinement |
---|---|
Similar structure data |
-
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 natural source / Source: (natural) ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.93 % |
---|---|
Crystal grow | Temperature: 293.5 K / Method: batch mode / pH: 7 / Details: Tris-HCl, Ammonium sulfate, Magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 297 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Nov 10, 2019 / Details: Kirkpatrick-Baez mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2782 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→70.9 Å / Num. obs: 47004 / % possible obs: 100 % / Redundancy: 346.2 % / CC1/2: 0.934777 / CC star: 0.9397 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 124.5 % / Mean I/σ(I) obs: 3 / Num. unique obs: 4650 / CC1/2: 0.7908 / CC star: 0.9397 / % possible all: 100 |
Serial crystallography measurement | XFEL pulse repetition rate: 30 Hz |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Sample dehydration prevention: polyimide sealing / Sample holding: viscous medium / Support base: x-y translation stage |
Serial crystallography data reduction | Frame hits: 33438 / Frames indexed: 22412 / Frames total: 55307 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5ZYE Resolution: 1.75→70.623 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.51
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.8 Å2 / Biso mean: 13.1837 Å2 / Biso min: 1.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→70.623 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
|