2YDT | pdb_00002ydt

STRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A from FUSARIUM Graminearum in complexe with an iminosugar inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2YDT/pdb

• Classification: HYDROLASE
• Organism(s): Fusarium graminearum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-24 Released: 2011-07-13 
• Deposition Author(s): Goddard-Borger, E.D., Carapito, R., Jeltsch, J.M., Phalip, V., Stick, R.V., Varrot, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Alpha-L-Arabinofuranosylated Pyrrolidines as Arabinanase Inhibitors.

Goddard-Borger, E.D., Carapito, R., Jeltsch, J., Phalip, V., Stick, R.V., Varrot, A.

(2011) Chem Commun (Camb) 47: 9684

• PubMed: 21773614 
• DOI: https://doi.org/10.1039/c1cc13675e
• Primary Citation Related Structures: 
  2YDP, 2YDT


• PubMed Abstract: 
  

  As part of continued efforts to understand the mechanisms of 1,5-α-l-arabinanases better, some arabinan-like iminosugar oligosaccharides were synthesized. An iminosugar analogue of arabinobiose was found to be a good inhibitor of the arabinanase Arb93A from Fusarium graminearum. Structures were determined for complexes of this inhibitor with wild-type Arb93A and a catalytically inactive mutant.

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Organizational Affiliation: 
• School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.

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: 42.22 kDa 
• Atom Count: 3,495 
• Modeled Residue Count: 359 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE	A	367	Fusarium graminearum	Mutation(s): 0  EC: 3.2.1.55
UniProt
Find proteins for B8ZY56 (Gibberella zeae) Explore B8ZY56  Go to UniProtKB:  B8ZY56

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AHR	C [auth A]	alpha-L-arabinofuranose C5 H10 O5 HMFHBZSHGGEWLO-QMKXCQHVSA-N
EDG	B [auth A]	1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL C5 H11 N O3 OQEBIHBLFRADNM-YUPRTTJUSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	N [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.435	α = 90
b = 105.435	β = 90
c = 140.038	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Goddard-Borger, E.D., Carapito, R., Jeltsch, J.M., Phalip, V., Stick, R.V., Varrot, A.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2011-11-16
  Changes: Database references, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary