[English] 日本語
![](img/lk-miru.gif)
- PDB-7zo0: Crystal structure of catalytic inactive unliganded form of FucOB,... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7zo0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of catalytic inactive unliganded form of FucOB, a GH95 family alpha-1,2-fucosidase from Akkermansia muciniphila | ||||||
![]() | GH95 family alpha-1,2-fucosidase | ||||||
![]() | HYDROLASE / Glycosyl hydrolase Fucosidase Akkermansia muciniphila Mucin Bombay blood group Blood conversion | ||||||
Function / homology | Alpha-L-fucosidase / Glycosyl hydrolase family 95, N-terminal domain / Glycosyl hydrolase family 65, N-terminal domain / alpha-L-fucosidase activity / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / Glycosyl hydrolase family 95 N-terminal domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Anso, I. / Cifuente, J.O. / Trastoy, B. / Guerin, M.E. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Turning universal O into rare Bombay type blood. Authors: Anso, I. / Naegeli, A. / Cifuente, J.O. / Orrantia, A. / Andersson, E. / Zenarruzabeitia, O. / Moraleda-Montoya, A. / Garcia-Alija, M. / Corzana, F. / Del Orbe, R.A. / Borrego, F. / Trastoy, ...Authors: Anso, I. / Naegeli, A. / Cifuente, J.O. / Orrantia, A. / Andersson, E. / Zenarruzabeitia, O. / Moraleda-Montoya, A. / Garcia-Alija, M. / Corzana, F. / Del Orbe, R.A. / Borrego, F. / Trastoy, B. / Sjogren, J. / Guerin, M.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 166.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 124.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7znzSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 87382.805 Da / Num. of mol.: 1 / Mutation: E541A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc Gene: Amuc_1120 / Plasmid: pET29a / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM sodium chloride, 20% (w/v) PEG 3350 (PEG ION suite protein crystallization screening, Hampton Research) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→52.24 Å / Num. obs: 423928 / % possible obs: 99.84 % / Redundancy: 6.8 % / Biso Wilson estimate: 27.38 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1299 / Rpim(I) all: 0.05409 / Rrim(I) all: 0.1409 / Net I/σ(I): 12.84 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 43184 / CC1/2: 0.648 / CC star: 0.887 / Rpim(I) all: 0.4985 / Rrim(I) all: 1.323 / % possible all: 99.77 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7ZNZ Resolution: 1.95→52.24 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.01 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→52.24 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|