8WOK | pdb_00008wok

Crystal structure of PL7 family alginate lyase AlyMc

• PDB DOI: https://doi.org/10.2210/pdb8WOK/pdb

• Classification: LYASE
• Organism(s): Saccharina japonica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-07 Released: 2024-10-16 
• Deposition Author(s): Yang, M., Mou, H.J., Kong, Q.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.171 (DCC) 

Starting Model: in silico

Literature

Crystal structure of PL7 family alginate lyase AlyMc

Yang, M., Mou, H.J., Kong, Q.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.67 kDa 
• Atom Count: 4,795 
• Modeled Residue Count: 554 
• Deposited Residue Count: 568 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PL7 alignate lyase	A	284	Saccharina japonica	Mutation(s): 0
UniProt
Find proteins for A0A1Q2M1X9 (Microbulbifer agarilyticus) Explore A0A1Q2M1X9  Go to UniProtKB:  A0A1Q2M1X9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PL7 alignate lyase	B	284	Saccharina japonica	Mutation(s): 0
UniProt
Find proteins for A0A1Q2M1X9 (Microbulbifer agarilyticus) Explore A0A1Q2M1X9  Go to UniProtKB:  A0A1Q2M1X9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.171 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.44	α = 90
b = 65.013	β = 95.073
c = 82.182	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Yang, M., Mou, H.J., Kong, Q.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release