Download MendeleyTruncated beta-galactosidase III from Bifidobacterium bifidum
Nielsen, J.A., Andersen, J.L., Alsarraf, H., Blaise, M., Thirup, S.S., Larsen, M.K., Cramer, J.F.To be published.
6QUD
2-deoxy-galactose reaction intermediate of a Truncated beta-galactosidase III from Bifidobacterium bifidum
- PDB DOI: https://doi.org/10.2210/pdb6QUD/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Bifidobacterium bifidum
- Expression System: Bacillus subtilis
- Mutation(s): No
- Deposited: 2019-02-27 Released: 2020-03-18
- Funding Organization(s): Danish Agency for Science Technology and Innovation
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.209
- R-Value Work: 0.165
- R-Value Observed: 0.167
Starting Model: experimental
View more details
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-galactosidase | 885 | Bifidobacterium bifidum | Mutation(s): 0 EC: 3.2.1.23 |  | |
UniProt | |||||
Find proteins for Q9F4D5 (Bifidobacterium bifidum) Explore Q9F4D5 Go to UniProtKB: Q9F4D5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9F4D5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2DG (Subject of Investigation/LOI) Query on 2DG | B [auth A] | 2-deoxy-alpha-D-galactopyranose C6 H12 O5 PMMURAAUARKVCB-ARQDHWQXSA-N |  | ||
| CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.209
- R-Value Work: 0.165
- R-Value Observed: 0.167
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 70.21 | α = 90 |
| b = 53.92 | β = 106.59 |
| c = 112.62 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-03-18 Deposition Author(s): Thirup, S.S., Nielsen, J.A., Andersen, J.L., Alsarraf, H., Blaise, M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Danish Agency for Science Technology and Innovation | Denmark | -- |
Revision History (Full details and data files)
- Version 1.0: 2020-03-18
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Derived calculations, Structure summary - Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary - Version 1.3: 2024-11-13
Changes: Structure summary
