5ZN7 | pdb_00005zn7

Crystal structure of GH31 alpha-xylosidase from a soil metagenome complexed with xylose

• PDB DOI: https://doi.org/10.2210/pdb5ZN7/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: 2.10 Å
• R-Value Free: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

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  (Explore in 3D)
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  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 627.74 kDa 
• Atom Count: 47,562 
• Modeled 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
XYS	I [auth A], J [auth C], K [auth D], L [auth F], M [auth H]	alpha-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-LECHCGJUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.915	α = 90
b = 124.865	β = 116.98
c = 177.716	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
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Structure summary