2GFT
Crystal structure of the E263A nucleophile mutant of Bacillus licheniformis endo-beta-1,4-galactanase in complex with galactotriose
- PDB DOI: https://doi.org/10.2210/pdb2GFT/pdb
- Classification: HYDROLASE
- Organism(s): Bacillus licheniformis
- Expression System: Bacillus subtilis
- Mutation(s): Yes
- Deposited: 2006-03-23 Released: 2006-06-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.232
- R-Value Work: 0.180
- R-Value Observed: 0.183
wwPDB Validation 3D Report Full Report
This is version 2.2 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 53 | 399 | Bacillus licheniformis | Mutation(s): 1 EC: 3.2.1.89 |  | |
UniProt | |||||
Find proteins for Q65CX5 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65CX5 Go to UniProtKB: Q65CX5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q65CX5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CA Query on CA | E [auth A], F [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900114 Query on PRD_900114 | C, D | 4beta-beta-galactotriose | Oligosaccharide / Metabolism |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.232
- R-Value Work: 0.180
- R-Value Observed: 0.183
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.273 | α = 90 |
| b = 79.354 | β = 100.56 |
| c = 103.906 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2006-06-13 Deposition Author(s): Welner, D., Le Nours, J., De Maria, L., Jorgensen, C.T., Christensen, L.L.H., Larsen, S., Lo Leggio, L.
Revision History (Full details and data files)
- Version 1.0: 2006-06-13
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2018-01-24
Changes: Data collection, Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2021-10-20
Changes: Database references, Structure summary - Version 2.2: 2024-02-14
Changes: Data collection, Refinement description
