8BXZ

Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with penta-mannuronic acid

• PDB DOI: https://doi.org/10.2210/pdb8BXZ/pdb

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


• Deposited: 2022-12-11 Released: 2023-12-20 
• Deposition Author(s): Wilkens, C.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.141 
• R-Value Work: 0.115 
• R-Value Observed: 0.116 

Starting Model: experimental

Literature

Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with penta-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: 26.52 kDa 
• Atom Count: 2,341 
• 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): 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)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid	B	5		N/A
Glycosylation Resources
GlyTouCan:  G61688UV GlyCosmos:  G61688UV

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.141 
• R-Value Work: 0.115 
• R-Value Observed: 0.116 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.23	α = 74.74
b = 39.99	β = 78.48
c = 42.72	γ = 69.51

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Wilkens, C.

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Funding Organization	Location	Grant Number
Other government	Denmark	--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release