5ZN6

Crystal structure of GH31 alpha-xylosidase from a soil metagenome

• PDB DOI:  https://doi.org/10.2210/pdb5ZN6/pdb

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


• Deposited: 2018-04-07 Released: 2019-04-10 
• Deposition Author(s): Matsuzawa, T., Nakamichi, Y., Watanabe, M., Yaoi, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Literature

Structural insight into substrate specificity of alpha-xylosidase from a soil metagenome

Matsuzawa, T., Nakamichi, Y., Watanabe, M., Yaoi, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 631.78 kDa 
• Atom Count: 47,599 
• Modelled Residue Count: 5,421 
• Deposited Residue Count: 5,496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-xylosidase MeXyl31	A, B, C, D, E, F, G [auth H], H [auth G]	687	soil metagenome	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	AA [auth C], AB [auth H], BA [auth C], BB [auth H], CA [auth C], CB [auth G], DA [auth C], DB [auth G], EA [auth C], EB [auth G], FA [auth C], FB [auth G], GA [auth C], GB [auth G], HA [auth D], HB [auth G], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth E], O [auth A], OA [auth E], P [auth A], PA [auth E], Q [auth A], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth H], V [auth B], VA [auth H], W [auth B], WA [auth H], X [auth B], XA [auth H], Y [auth B], YA [auth H], Z [auth C], ZA [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.146	α = 90
b = 124.174	β = 116.81
c = 177.453	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Matsuzawa, T., Nakamichi, Y., Watanabe, M., Yaoi, K.

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release