8KHV | pdb_00008khv

The crystal structure of glycosaminoglycan lyase GAGase II

• PDB DOI: https://doi.org/10.2210/pdb8KHV/pdb

• Classification: LYASE
• Organism(s): Spirosoma fluviale
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-22 Released: 2024-09-04 
• Deposition Author(s): Wei, L., Cao, H.Y., Li, F.C.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

The crystal structure of glycosaminoglycan lyase GAGase VII

Wei, L., Cao, H.Y., Li, F.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: 68.63 kDa 
• Atom Count: 5,177 
• Modeled Residue Count: 579 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparinase II/III-like protein	A	614	Spirosoma fluviale	Mutation(s): 0  Gene Names: SAMN06269250_2316
UniProt
Find proteins for A0A286FIB6 (Spirosoma fluviale) Explore A0A286FIB6  Go to UniProtKB:  A0A286FIB6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.917	α = 90
b = 82.096	β = 106.59
c = 79.885	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Wei, L., Cao, H.Y., Li, F.C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31570071
National Science Foundation (NSF, China)	China	31971201

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release