5JRN

Crystal Structure of a Xylanase in Complex with a Monosaccharide at 2.84 Angstroem resolution

• PDB DOI: https://doi.org/10.2210/pdb5JRN/pdb

• Classification: HYDROLASE
• Organism(s): Fusarium oxysporum f. sp. vasinfectum 25433
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-06 Released: 2017-05-24 
• Deposition Author(s): Gomez, S., Payne, A.M., Savko, M., Fox, G.C., Shepard, W.E., Fernandez, F.J., Vega, M.C.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.226 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 22.05 kDa 
• Atom Count: 1,547 
• Modelled Residue Count: 189 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A	194	Fusarium oxysporum f. sp. vasinfectum 25433	Mutation(s): 0  Gene Names: FOTG_15646 EC: 3.2.1.8
UniProt
Find proteins for X0M5X0 (Fusarium oxysporum f. sp. vasinfectum 25433) Explore X0M5X0  Go to UniProtKB:  X0M5X0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6MJ	I [auth A]	methyl beta-D-xylopyranoside C6 H12 O5 ZBDGHWFPLXXWRD-JGWLITMVSA-N
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.226 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.7	α = 90
b = 36.1	β = 90
c = 48.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Gomez, S., Payne, A.M., Savko, M., Fox, G.C., Shepard, W.E., Fernandez, F.J., Vega, M.C.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	PET2008_0101
Spanish Ministry of Economy and Competitiveness	Spain	BIO2009-11184
Spanish Ministry of Economy and Competitiveness	Spain	BFU2010-22260-C02-2
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2015-66206-C2-2-R
European Union	Spain	ComplexINC No. 279039

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary