6ZJ6
Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with cyclohexylmethyl-Glc-1,3-isofagomine
- PDB DOI: https://doi.org/10.2210/pdb6ZJ6/pdb
- Classification: HYDROLASE
- Organism(s): Bacteroides xylanisolvens XB1A
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-06-27 Released: 2020-11-18
- Funding Organization(s): European Research Council (ERC), Australian Research Council (ARC), Biotechnology and Biological Sciences Research Council (BBSRC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.09 Å
- R-Value Free: 0.136
- R-Value Work: 0.113
This is version 2.1 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glycosyl hydrolase family 71 | A [auth AAA] | 385 | Bacteroides xylanisolvens XB1A | Mutation(s): 0 Gene Names: BXY_34140 |  |
UniProt | |||||
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Explore D6D1V7 Go to UniProtKB: D6D1V7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D6D1V7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GLC (Subject of Investigation/LOI) Query on GLC | I [auth AAA] | alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N |  | ||
| IFM (Subject of Investigation/LOI) Query on IFM | H [auth AAA] | 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE C6 H13 N O3 QPYJXFZUIJOGNX-HSUXUTPPSA-N |  | ||
| QTE (Subject of Investigation/LOI) Query on QTE | G [auth AAA] | methylcyclohexane C7 H14 UAEPNZWRGJTJPN-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | B [auth AAA], C [auth AAA], D [auth AAA], E [auth AAA] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | F [auth AAA] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.09 Å
- R-Value Free: 0.136
- R-Value Work: 0.113
- Space Group: I 4
- Diffraction Data: https://doi.org/10.5281/zenodo.4288341
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 107.981 | α = 90 |
| b = 107.981 | β = 90 |
| c = 67.282 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| xia2 | data reduction |
| Aimless | data scaling |
| REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-11-18 Deposition Author(s): Thompson, A.J., Sobala, L.F., Fernandes, P.Z., Hakki, Z., Howe, J.D., Hill, M., Zitzmann, N., Davies, S., Stamataki, Z., Butters, T.D., Alonzi, D.S., Williams, S.J., Davies, G.J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| European Research Council (ERC) | United Kingdom | 322942 |
| Australian Research Council (ARC) | Australia | DP120101396 |
| Australian Research Council (ARC) | Australia | FT130100103 |
| Australian Research Council (ARC) | Australia | DP180101957 |
| Biotechnology and Biological Sciences Research Council (BBSRC) | United Kingdom | BB/G016127/1 |
Revision History (Full details and data files)
- Version 1.0: 2020-11-18
Type: Initial release - Version 1.1: 2020-12-02
Changes: Database references - Version 2.0: 2021-01-20
Changes: Atomic model, Data collection, Database references, Derived calculations - Version 2.1: 2024-01-31
Changes: Data collection, Database references, Derived calculations, Refinement description
