8QMJ

Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124 soaked with hexa-mannuronic acid

• PDB DOI: https://doi.org/10.2210/pdb8QMJ/pdb

• Classification: LYASE
• Organism(s): Paradendryphiella salina
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2023-09-22 Released: 2024-10-02 
• Deposition Author(s): Wilkens, C.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.157 
• R-Value Work: 0.134 
• R-Value Observed: 0.134 

Starting Model: experimental

Literature

Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124 soaked with with hexa-mannuronic acid

Wilkens, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.07 kDa 
• Atom Count: 2,306 
• Modelled Residue Count: 228 
• 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): 1  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)-beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid	B	4		N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.157 
• R-Value Work: 0.134 
• R-Value Observed: 0.134 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.35	α = 90
b = 38.75	β = 116.9
c = 75.01	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Wilkens, C.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release