8PED

Crystal structure of Paradendryphiella salina PL7C alginate lyase soaked with trimannuronic acid

• PDB DOI: https://doi.org/10.2210/pdb8PED/pdb

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


• Deposited: 2023-06-13 Released: 2023-07-12 
• Deposition Author(s): Wilkens, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.146 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 

Starting Model: experimental

Literature

Crystal structure of Paradendryphiella salina PL7C alginate lyase soaked with trimannuronic acid

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.67 kDa 
• Atom Count: 2,265 
• Modelled Residue Count: 230 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase	A	234	Paradendryphiella salina	Mutation(s): 0  Gene Names: PsAlg7C
UniProt
Find proteins for A0A7I9C8Z1 (Paradendryphiella salina) Explore A0A7I9C8Z1  Go to UniProtKB:  A0A7I9C8Z1

Oligosaccharides

Help

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid	C	3		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.146 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.06	α = 90
b = 59.77	β = 90
c = 89.34	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Wilkens, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection