Download MendeleyStructure and activity of the GH20 beta-N-beta-N-acetylhexosaminidase from Bifidobacterium bifidum
He, Y., Jin, Y.To be published.
6YXZ
Structure and activity of the GH20 beta-N-beta-N-acetylhexosaminidase from Bifidobacterium bifidum
- PDB DOI: https://doi.org/10.2210/pdb6YXZ/pdb
- Classification: HYDROLASE
- Organism(s): Bifidobacterium bifidum
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-05-04 Released: 2021-05-12
- Funding Organization(s): Wellcome Trust, National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.220
- R-Value Work: 0.160
Starting Model: other
View more details
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-N-acetylhexosaminidase | A [auth JJJ] | 1,010 | Bifidobacterium bifidum | Mutation(s): 0 Gene Names: bbhII, B0085_1802, LMG11583_1629 EC: 3.2.1.52 |  |
UniProt | |||||
Find proteins for D4QAP5 (Bifidobacterium bifidum) Explore D4QAP5 Go to UniProtKB: D4QAP5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D4QAP5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | B [auth JJJ] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NI Query on NI | F [auth JJJ] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth JJJ] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | C [auth JJJ], D [auth JJJ] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.220
- R-Value Work: 0.160
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.566 | α = 90 |
| b = 126.75 | β = 90 |
| c = 152.71 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DIALS | data reduction |
| Aimless | data scaling |
| SHELXDE | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| Wellcome Trust | United Kingdom | 209057/Z/ 17/Z |
| National Natural Science Foundation of China (NSFC) | China | 31400663 |
Revision History (Full details and data files)
- Version 1.0: 2021-05-12
Type: Initial release - Version 1.1: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2024-11-13
Changes: Structure summary
