7YQS

Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex

• PDB DOI:  https://doi.org/10.2210/pdb7YQS/pdb

• Classification: LYASE
• Organism(s): Fusarium oxysporum
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2022-08-08 Released: 2023-08-09 
• Deposition Author(s): Yano, N., Kondo, T., Kusaka, K., Yamada, T., Arakawa, T., Sakamoto, T., Fushinobu, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.163 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 

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• Method: NEUTRON DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.191 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed by neutron crystallography

Yano, N., Kondo, T., Kusaka, K., Yamada, T., Arakawa, T., Sakamoto, T., Fushinobu, S.

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: 51.73 kDa 
• Atom Count: 3,743 
• Modelled Residue Count: 419 
• Deposited Residue Count: 443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-RHAMNOSE-ALPHA-1,4-D-GLUCURONATE LYASE	A	443	Fusarium oxysporum	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL GlyCosmos:  G55220VL GlyGen:  G55220VL

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAM (Subject of Investigation/LOI)	C [auth A]	alpha-L-rhamnopyranose C6 H12 O5 SHZGCJCMOBCMKK-HGVZOGFYSA-N
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.163 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 
• Space Group: P 2₁ 2₁ 2₁

• Method: NEUTRON DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.191 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.78	α = 90
b = 65.8	β = 90
c = 108.95	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	refinement
STARGazer	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Yano, N., Kondo, T., Kusaka, K., Yamada, T., Arakawa, T., Sakamoto, T., Fushinobu, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H00929
Japan Society for the Promotion of Science (JSPS)	Japan	15H02443
Japan Society for the Promotion of Science (JSPS)	Japan	26660083

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release