4AD3

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with Glucose-1,3-deoxymannojirimycin

• PDB DOI: https://doi.org/10.2210/pdb4AD3/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides xylanisolvens XB1A
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-12-21 Released: 2012-02-01 
• Deposition Author(s): Thompson, A.J., Williams, R.J., Hakki, Z., Alonzi, D.S., Wennekes, T., Gloster, T.M., Songsrirote, K., Thomas-Oates, J.E., Wrodnigg, T.M., Spreitz, J., Stuetz, A.E., Butters, T.D., Williams, S.J., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 175.29 kDa 
• Atom Count: 12,473 
• Modelled Residue Count: 1,377 
• Deposited Residue Count: 1,520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSYL HYDROLASE FAMILY 71	A, B, C, D	380	Bacteroides xylanisolvens XB1A	Mutation(s): 0  EC: 3.2.1.130
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Explore D6D1V7  Go to UniProtKB:  D6D1V7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	E [auth A], G [auth B], I [auth C], K [auth D]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
DMJ	F [auth A], H [auth B], J [auth C], L [auth D]	1-DEOXYMANNOJIRIMYCIN C6 H13 N O4 LXBIFEVIBLOUGU-KVTDHHQDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 222.478	α = 90
b = 222.478	β = 90
c = 84.715	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Thompson, A.J., Williams, R.J., Hakki, Z., Alonzi, D.S., Wennekes, T., Gloster, T.M., Songsrirote, K., Thomas-Oates, J.E., Wrodnigg, T.M., Spreitz, J., Stuetz, A.E., Butters, T.D., Williams, S.J., Davies, G.J.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2012-02-29
  Changes: Other
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary