7R2X | pdb_00007r2x

Paradendryphiella salina PL8 mannuronate-specific alginate lyase

• PDB DOI: https://doi.org/10.2210/pdb7R2X/pdb

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


• Deposited: 2022-02-06 Released: 2023-02-15 
• Deposition Author(s): Fredslung, F., Welner, D.H., Wilkens, C.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.245 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: in silico

Literature

Paradendryphiella salina PL8 mannuronate-specific alginate lyase

Fredslung, 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 172.29 kDa 
• Atom Count: 11,928 
• Modeled Residue Count: 1,524 
• Deposited Residue Count: 1,546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannuronic acid specific lyase	A, B	773	Paradendryphiella salina	Mutation(s): 0  Gene Names: PsMan8A
UniProt
Find proteins for A0A5Q5AD67 (Paradendryphiella salina) Explore A0A5Q5AD67  Go to UniProtKB:  A0A5Q5AD67
Glycosylation
Glycosylation Sites: 4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free:  0.245 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.89	α = 90
b = 108.89	β = 90
c = 150.49	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Fredslung, F., Welner, D.H., Wilkens, C.

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Funding Organization	Location	Grant Number
European Commission	European Union	9082-00021B

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary