[English] 日本語
![](img/lk-miru.gif)
- PDB-1gyh: Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1gyh | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant | ||||||
![]() | ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A | ||||||
![]() | HYDROLASE / ARABINANASE / PROPELLER / CATALYSIS / CELLVIBRIO / PSEUDOMONAS | ||||||
Function / homology | ![]() arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / McKie, V.A. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J. | ||||||
![]() | ![]() Title: Cellovibrio Cellulosa Alpha-L-Arabinanase 43A Has a Novel Five-Blade Beta-Propeller Fold Authors: Nurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / Mckie, V.A. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 808.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 672.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.7 KB | Display | |
Data in XML | ![]() | 38.9 KB | Display | |
Data in CIF | ![]() | 67.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 36146.512 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ENGINEERED MUTATION ASP 158 ALA / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P95470*PLUS, arabinan endo-1,5-alpha-L-arabinanase #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.9 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: 18% PEG5000 MME, 4% AMMONIUM SULFATE, 100MM NA-CACODYLATE PH6.5, 20% GLYCEROL, pH 6.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 155379 / % possible obs: 97.4 % / Redundancy: 1.89 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.37 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.08 / % possible all: 89.8 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Redundancy: 1.9 % |
Reflection shell | *PLUS % possible obs: 89.8 % / Redundancy: 1.8 % / Mean I/σ(I) obs: 3.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: MAP FROM AN A P6522 CRYSTAL FORM SOLVED BY MAD Resolution: 1.89→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.191 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.75 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|