7OOF

Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with tri-mannuronic acid

• PDB DOI: https://doi.org/10.2210/pdb7OOF/pdb

• Classification: LYASE
• Organism(s): Paradendryphiella salina
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2021-05-27 Released: 2022-06-08 
• Deposition Author(s): Fredslund, F., Welner, D.H., Wilkens, C.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.174 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with tri-mannuronic acid

Fredslund, F., Welner, D.H., Wilkens, C.

To be published.

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: 26.4 kDa 
• Atom Count: 2,124 
• Modelled Residue Count: 226 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase (PL7)	A	231	Paradendryphiella salina	Mutation(s): 0  Gene Names: PsAlg7A
UniProt
Find proteins for A0A485PVH1 (Paradendryphiella salina) Explore A0A485PVH1  Go to UniProtKB:  A0A485PVH1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid	B	3		N/A
Glycosylation Resources
GlyTouCan:  G85027VZ GlyCosmos:  G85027VZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MAV (Subject of Investigation/LOI)	C [auth A]	alpha-D-mannopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-BYHBOUFCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.174 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.81	α = 90
b = 81.11	β = 90
c = 80.69	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
Coot	model building
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Fredslund, F., Welner, D.H., Wilkens, C.

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Funding Organization	Location	Grant Number
European Union (EU)	Denmark	9082-00021B

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary