1Y65
Crystal structure of beta-hexosaminidase from Vibrio cholerae in complex with N-acetyl-D-glucosamine to a resolution of 1.85
- PDB DOI: https://doi.org/10.2210/pdb1Y65/pdb
- Classification: HYDROLASE
- Organism(s): Vibrio cholerae
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2004-12-03 Released: 2004-12-14
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.209
- R-Value Work: 0.157
- R-Value Observed: 0.157
This is version 1.6 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 |
| Beta-hexosaminidase | 342 | Vibrio cholerae | Mutation(s): 0 Gene Names: nagZ EC: 3.2.1.52 |  | |
UniProt | |||||
Find proteins for Q9KU37 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KU37 Go to UniProtKB: Q9KU37 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9KU37 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | B [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.209
- R-Value Work: 0.157
- R-Value Observed: 0.157
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 48.524 | α = 90 |
| b = 81.203 | β = 90 |
| c = 86.495 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| AMoRE | phasing |
Entry History
Deposition Data
- Released Date: 2004-12-14 Deposition Author(s): Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2004-12-14
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2017-10-11
Changes: Refinement description - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary - Version 1.5: 2021-02-03
Changes: Structure summary - Version 1.6: 2023-08-23
Changes: Data collection, Database references, Refinement description
