8KHW | pdb_00008khw

The crystal structure of glycosaminoglycan lyase GAGase VII

• PDB DOI: https://doi.org/10.2210/pdb8KHW/pdb

• Classification: LYASE
• Organism(s): Bacteroides intestinalis
• 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: 2.40 Å
• R-Value Free: 
  0.271 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.19 kDa 
• Atom Count: 4,674 
• Modeled Residue Count: 582 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF4962 domain-containing protein	A	618	Bacteroides intestinalis	Mutation(s): 0  Gene Names: EAJ06_20265
UniProt
Find proteins for A0A4V1YUP8 (Bacteroides intestinalis) Explore A0A4V1YUP8  Go to UniProtKB:  A0A4V1YUP8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.271 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.407	α = 90
b = 98.407	β = 90
c = 134.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	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