6A40

complex structure of Alginate lyase AlyF-OU02 with G4

• PDB DOI: https://doi.org/10.2210/pdb6A40/pdb

• Classification: LYASE
• Organism(s): Vibrio splendidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-18 Released: 2019-05-01 
• Deposition Author(s): Liu, W.Z., Lyu, Q.Q., Zhang, K.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.199 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

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: gel filtration

Macromolecule Content

• Total Structure Weight: 59.8 kDa 
• Atom Count: 4,295 
• Modelled Residue Count: 498 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alginate lyase AlyF-OU02	A	536	Vibrio splendidus	Mutation(s): 0
UniProt
Find proteins for A0A2S7V3I3 (Vibrio splendidus) Explore A0A2S7V3I3  Go to UniProtKB:  A0A2S7V3I3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid	B	4		N/A
Glycosylation Resources
GlyTouCan:  G72802WN GlyCosmos:  G72802WN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.199 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.212	α = 90
b = 106.212	β = 90
c = 100.846	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Liu, W.Z., Lyu, Q.Q., Zhang, K.K.

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2019-05-15
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary