7KNC

Crystal structure of the GH31 alpha-xylosidase (Xac1773) from Xanthomonas citri

• PDB DOI: https://doi.org/10.2210/pdb7KNC/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas citri pv. citri str. 306
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-11-04 Released: 2021-05-26 
• Deposition Author(s): Vieira, P.S., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors

Vieira, P.S., Bonfim, I.M., Araujo, E.A., Melo, R.R., Lima, A.R., Fessel, M.R., Paixao, D.A.A., Persinoti, G.F., Rocco, S.A., Lima, T.B., Pirolla, R.A.S., Morais, M.A.B., Correa, J.B.L., Zanphorlin, L.M., Diogo, J.A., Lima, E.A., Grandis, A., Buckeridge, M.S., Gozzo, F.C., Benedetti, C.E., Polikarpov, I., Giuseppe, P.O., Murakami, M.T.

(2021) Nature Communications 12: 4049

• DOI: https://doi.org/10.1038/s41467-021-24277-4

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 111.33 kDa 
• Atom Count: 8,159 
• Modelled Residue Count: 919 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-xylosidase	A	988	Xanthomonas citri pv. citri str. 306	Mutation(s): 1  Gene Names: xylS, XAC1773

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYS (Subject of Investigation/LOI)	C [auth A]	alpha-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-LECHCGJUSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.493	α = 90
b = 146.632	β = 90
c = 63.044	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Vieira, P.S., Murakami, M.T.

---

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2016/06509-0
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/26982-0

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description