8E1W | pdb_00008e1w

Neutron crystal structure of Panus similis AA9A at room temperature

• PDB DOI: https://doi.org/10.2210/pdb8E1W/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Panus similis
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2022-08-11 Released: 2023-01-11 
• Deposition Author(s): Meilleur, F., Tandrup, T., Lo Leggio, L.
• Funding Organization(s): Novo Nordisk Foundation, Danish Council for Independent Research, National Institute of Food and Agriculture (NIFA, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.260 (Depositor) 
• R-Value Work: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Joint X-ray/neutron structure of Lentinus similis AA9_A at room temperature.

Tandrup, T., Lo Leggio, L., Meilleur, F.

(2023) Acta Crystallogr F Struct Biol Commun 79: 1-7

• PubMed: 36598350 
• DOI: https://doi.org/10.1107/S2053230X22011335
• Primary Citation of Related Structures:  
  8E1W


• PubMed Abstract: 
  

  Lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes which cleave polysaccharides oxidatively and are important in pathogen biology, carbon cycling and biotechnology. The Lentinus similis family AA9 isoform A (LsAA9_A) has been extensively studied as a model system because its activity towards smaller soluble saccharide substrates has allowed detailed structural characterization of its interaction with a variety of substrates by X-ray crystallography at high resolution. Here, the joint X-ray/neutron room-temperature crystallographic structure of carbohydrate-free LsAA9_A in the copper(II) resting state refined against X-ray and neutron data at 2.1 and 2.8 Å resolution, respectively, is presented. The results provide an experimental determination of the protonation states of the copper(II)-coordinating residues and second-shell residues in LsAA9_A, paving the way for future neutron crystallographic studies of LPMO-carbohydrate complexes.

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Organizational Affiliation: 
• Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, NC 27695, USA.

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: 25.59 kDa 
• Atom Count: 1,931 
• Modeled Residue Count: 235 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-beta-1,4-glucanase D	A	235	Panus similis	Mutation(s): 0  EC: 3.2.1.4 (PDB Primary Data), 1.14.99.56 (UniProt)
UniProt
Find proteins for A0A0S2GKZ1 (Panus similis) Explore A0A0S2GKZ1  Go to UniProtKB:  A0A0S2GKZ1
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU (Subject of Investigation/LOI)	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.260 (Depositor) 
• R-Value Work:  0.225 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.469	α = 90
b = 126.469	β = 90
c = 126.469	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Mantid	data reduction
LAUENORM	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Meilleur, F., Tandrup, T., Lo Leggio, L.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF17SA0027704
Danish Council for Independent Research	Denmark	8021-00273B
National Institute of Food and Agriculture (NIFA, United States)	United States	Hatch211001

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 2.0: 2023-01-18
  Changes: Atomic model
• Version 2.1: 2024-04-03
  Changes: Data collection, Refinement description