5ZKW

Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 in complex with GF2

• PDB DOI: https://doi.org/10.2210/pdb5ZKW/pdb

• Classification: HYDROLASE
• Organism(s): Pseudarthrobacter chlorophenolicus A6
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-03-26 Released: 2018-12-19 
• Deposition Author(s): Yu, S.H., Shen, H., Li, X., Mu, W.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Structural and functional basis of difructose anhydride III hydrolase, which sequentially converts inulin using the same catalytic residue

Yu, S.H., Shen, H., Cheng, Y.Y., Zhu, Y.Y., Li, X., Mu, W.M.

(2018) ACS Catal 8: 10683-10697

• DOI: https://doi.org/10.1021/acscatal.8b02424

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 285.21 kDa 
• Atom Count: 20,591 
• Modelled Residue Count: 2,545 
• Deposited Residue Count: 2,670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DFA-IIIase	A, B, C [auth D], D [auth C], E, F	445	Pseudarthrobacter chlorophenolicus A6	Mutation(s): 0  Gene Names: Achl_2895 EC: 3.2.1
UniProt
Find proteins for B8HDZ1 (Pseudarthrobacter chlorophenolicus (strain ATCC 700700 / DSM 12829 / CIP 107037 / JCM 12360 / KCTC 9906 / NCIMB 13794 / A6)) Explore B8HDZ1  Go to UniProtKB:  B8HDZ1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose	G, H, I, J	3		N/A
Glycosylation Resources
GlyTouCan:  G11260CN GlyCosmos:  G11260CN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.121	α = 90
b = 79.233	β = 100.38
c = 140.571	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Yu, S.H., Shen, H., Li, X., Mu, W.M.

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations, Structure summary