[English] 日本語
![](img/lk-miru.gif)
- PDB-6jg2: Crystal structure of barley exohydrolaseI wildtype in complex wit... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6jg2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of barley exohydrolaseI wildtype in complex with 4'-nitrophenyl thiolaminaribioside | ||||||
![]() | Barley exohydrolase I | ||||||
![]() | HYDROLASE / Barley exohydrolaseI / enzyme function | ||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase / beta-glucosidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / membrane => GO:0016020 / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Luang, S. / Streltsov, V.A. / Hrmova, M. | ||||||
![]() | ![]() Title: The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases. Authors: Luang, S. / Fernandez-Luengo, X. / Nin-Hill, A. / Streltsov, V.A. / Schwerdt, J.G. / Alonso-Gil, S. / Ketudat Cairns, J.R. / Pradeau, S. / Fort, S. / Marechal, J.D. / Masgrau, L. / Rovira, C. / Hrmova, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 248.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 195.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jg1C ![]() 6jg6C ![]() 6jg7C ![]() 6jgaC ![]() 6jgbC ![]() 6jgcC ![]() 6jgdC ![]() 6jgeC ![]() 6jggC ![]() 6jgkC ![]() 6jglC ![]() 6jgnC ![]() 6jgoC ![]() 6jgpC ![]() 6jgqC ![]() 6jgrC ![]() 6jgsC ![]() 6jgtC ![]() 6k6vC ![]() 6kufC ![]() 6l1jC ![]() 6lbbC ![]() 6lbvC ![]() 6lc5C ![]() 3wliS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 3 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 65894.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() |
---|---|
#2: Sugar |
-Non-polymers , 5 types, 350 molecules ![](data/chem/img/BV6.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-BV6 / ( | ||||||
---|---|---|---|---|---|---|---|
#4: Chemical | ChemComp-1PE / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|---|
Sequence details | Lys320 is confirmed by DNA sequencing result. However, the electron density map is not clear, ...Lys320 is confirmed by DNA sequencing result. However, the electron density map is not clear, probably side chain of this residue is flexible. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.6 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1.7 M ammonium sulfate, 75 mM HEPES-NaOH buffer, pH 7, containing 7.5 mM sodium acetate and 1.2% (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 16, 2013 / Details: Osmic VariMax |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→87.82 Å / Num. obs: 58669 / % possible obs: 97.23 % / Redundancy: 24 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.835 / Num. unique obs: 4122 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3WLI Resolution: 2→41.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.341 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.01 Å2 / Biso mean: 42.362 Å2 / Biso min: 26.08 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→41.56 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|