8B5M | pdb_00008b5m

Crystal structure of GH47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with cyclosulfamidate inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8B5M/pdb

• Classification: HYDROLASE
• Organism(s): Caulobacter
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-23 Released: 2023-10-04 
• Deposition Author(s): Males, A., Davies, G.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 
  0.148 (Depositor), 0.147 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.136 (DCC) 

Starting Model: experimental

Literature

GH47 and Cyclosulfamidate

Males, A., Davies, G.J., Artola, M., Overkleeft, H.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.88 kDa 
• Atom Count: 4,288 
• Modeled Residue Count: 434 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannosyl-oligosaccharide 1,2-alpha-mannosidase	A	447	Caulobacter	Mutation(s): 0  Gene Names: Caul_4035 EC: 3.2.1.113
UniProt
Find proteins for B0SWV2 (Caulobacter sp. (strain K31)) Explore B0SWV2  Go to UniProtKB:  B0SWV2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5OV (Subject of Investigation/LOI)	B [auth A]	(3aR,4S,5S,6R,7R,7aS)-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3a,4,5,6,7,7a-hexahydro-3H-benzo[d][1,2,3]oxathiazole-4,5,6-triol C7 H13 N O7 S LDXSPHJOJCEWFB-MAFUWASYSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free:  0.148 (Depositor), 0.147 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.136 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.134	α = 90
b = 144.134	β = 90
c = 50.32	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Males, A., Davies, G.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T004819/1

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary