4PN2

Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri complexed with xylotriose

• PDB DOI: https://doi.org/10.2210/pdb4PN2/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas citri pv. citri str. 306
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-22 Released: 2014-10-08 
• Deposition Author(s): Santos, C.R., Martins, V.P.M., Zanphorlin, L.M., Ruller, R., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.240 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 69.64 kDa 
• Atom Count: 5,497 
• Modelled Residue Count: 610 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylanase	A, B	305	Xanthomonas citri pv. citri str. 306	Mutation(s): 0  Gene Names: xynB, XAC4254

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N
CA	C [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.240 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.284	α = 90
b = 83.199	β = 90.07
c = 72.05	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Santos, C.R., Martins, V.P.M., Zanphorlin, L.M., Ruller, R., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/13309-0

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2014-10-15
  Changes: Database references, Structure summary
• Version 1.2: 2014-11-26
  Changes: Database references
• Version 1.3: 2015-02-04
  Changes: Derived calculations
• Version 1.4: 2019-04-17
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.5: 2020-01-01
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2023-12-27
  Changes: Data collection, Database references, Structure summary