1Y65 | pdb_00001y65

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 
• Deposition Author(s): Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.209 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of beta-hexosaminidase from Vibrio cholerae in complex with N-acetyl-D-glucosamine to a resolution of 1.85

Gorman, J., Shapiro, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.09 kDa 
• Atom Count: 3,040 
• Modeled Residue Count: 330 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hexosaminidase	A	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

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 Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
AMoRE	phasing

Structure Validation

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  

• 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