[English] 日本語
![](img/lk-miru.gif)
- PDB-4a45: CpGH89CBM32-5, from Clostridium perfringens, in complex with GalN... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4a45 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CpGH89CBM32-5, from Clostridium perfringens, in complex with GalNAc- beta-1,3-galactose | |||||||||
![]() | ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN | |||||||||
![]() | HYDROLASE / FAMILY 89 GLYCOSIDE HYDROLASE / FAMILY 32 CARBOHYDRATE-BINDING MODULE | |||||||||
Function / homology | ![]() hydrolase activity, acting on glycosyl bonds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Ficko-Blean, E. / Stuart, C.P. / Suits, M.D. / Cid, M. / Tessier, M. / Woods, R.J. / Boraston, A.B. | |||||||||
![]() | ![]() Title: Carbohydrate Recognition by an Architecturally Complex Alpha-N-Acetylglucosaminidase from Clostridium Perfringens. Authors: Ficko-Blean, E. / Stuart, C.P. / Suits, M.D. / Cid, M. / Tessier, M. / Woods, R.J. / Boraston, A.B. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 47.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 31.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 760.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 761.8 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 13.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a3zC ![]() 4a41C ![]() 4a42C ![]() 4a44C ![]() 4a6oC ![]() 4aaxC ![]() 4a40 ![]() 4a43 C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17435.328 Da / Num. of mol.: 1 / Fragment: CBM32-5, RESIDUES 1356-1493 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q0TST1, UniProt: Q8XM24*PLUS, alpha-N-acetylglucosaminidase |
---|---|
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.74 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU-MSC R-AXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 14448 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.75→45.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.877 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.391 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→45.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|