6FAM
Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-2-aminodeoxymannojirimycin
- PDB DOI: https://doi.org/10.2210/pdb6FAM/pdb
- Classification: HYDROLASE
- Organism(s): Bacteroides xylanisolvens XB1A
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-12-15 Released: 2018-03-21
- Funding Organization(s): European Research Council, Australian Research Council
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.13 Å
- R-Value Free: 0.144
- R-Value Work: 0.122
- R-Value Observed: 0.123
This is version 1.4 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 | 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 | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MAN Query on MAN | C [auth A] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N |  | ||
| G63 Query on G63 | D [auth A] | mannose-alpha-1,3-2-aminodeoxymannojirimycin C6 H14 N2 O3 GFTGLZPGRKFGDU-KVTDHHQDSA-N |  | ||
| ACT Query on ACT | B [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.13 Å
- R-Value Free: 0.144
- R-Value Work: 0.122
- R-Value Observed: 0.123
- Space Group: I 4
- Diffraction Data: https://doi.org/10.5281/zenodo.4446244
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 108.101 | α = 90 |
| b = 108.101 | β = 90 |
| c = 67.507 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DIALS | data reduction |
| Aimless | data scaling |
| REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-03-21 Deposition Author(s): Fernandes, P.Z., Petricevic, M., Sobala, L.F., Davies, G.J., Williams, S.J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| European Research Council | United Kingdom | 322942 |
| Australian Research Council | Australia | FT130100103 |
| Australian Research Council | Australia | DP120101396 |
Revision History (Full details and data files)
- Version 1.0: 2018-03-21
Type: Initial release - Version 1.1: 2018-06-13
Changes: Data collection, Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2021-02-03
Changes: Data collection, Database references, Structure summary - Version 1.4: 2024-01-17
Changes: Data collection, Database references, Refinement description
