8AH3 | pdb_00008ah3

DG04279 glycoside hydrolase family 172

• PDB DOI: https://doi.org/10.2210/pdb8AH3/pdb

• Classification: HYDROLASE
• Organism(s): Dysgonomonas gade
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-20 Released: 2023-08-16 
• Deposition Author(s): Al-Jourani, O., Lowe, E.C., Basle, A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.162 (DCC) 

Starting Model: experimental

Literature

Mining the human gut microbiome identifies mycobacterial D-arabinan degrading enzymes

Al-Jourani, O., Benedict, S., Ross, J., Layton, A., van der Peet, P., Bailey, N.P., Heunis, T., Marando, V., Manion, J., Mensitieri, F., Abellon-Ruiz, J., Oram, S.L., Parsons, L., Cartmel, A., Wright, G.S.A., Basle, A., Trost, M., Kiessling, L.L., Henrissat, B., Munoz-Munoz, J., Lovering, A., Hirt, R.P., Williams, S.J., Lowe, E.C., Moynihan, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 43.51 kDa 
• Atom Count: 3,255 
• Modeled Residue Count: 375 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DG02479 GH127	A	378	Dysgonomonas gade	Mutation(s): 0  Gene Names: HMPREF9455_02479
UniProt
Find proteins for F5IZG2 (Dysgonomonas gadei ATCC BAA-286) Explore F5IZG2  Go to UniProtKB:  F5IZG2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.162 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.15	α = 90
b = 89.15	β = 90
c = 289.32	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
xia2	data scaling
pointless	data scaling
Aimless	data scaling
PHASER	phasing
Coot	model building
BUCCANEER	model building
MolProbity	model building
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Al-Jourani, O., Lowe, E.C., Basle, A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M011186/1
Royal Society	United Kingdom	RG/R2/202228

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary