6HAQ | pdb_00006haq

AFGH61B WILD-TYPE COPPER LOADED

• PDB DOI: https://doi.org/10.2210/pdb6HAQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus fumigatus Af293
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2018-08-08 Released: 2018-08-22 
• Deposition Author(s): Lo Leggio, L., Poulsen, J.C.N., Weihe, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.155 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.105 (Depositor), 0.105 (DCC) 
• R-Value Observed: 
  0.107 (Depositor) 

Starting Model: experimental

Literature

Structure of a lytic polysaccharide monooxygenase from Aspergillus fumigatus and an engineered thermostable variant.

Lo Leggio, L., Weihe, C.D., Poulsen, J.N., Sweeney, M., Rasmussen, F., Lin, J., De Maria, L., Wogulis, M.

(2018) Carbohydr Res 469: 55-59

• PubMed: 30296642 
• DOI: https://doi.org/10.1016/j.carres.2018.08.009
• Primary Citation Related Structures: 
  6H1Z, 6HA5, 6HAQ


• PubMed Abstract: 
  

  Lytic polysaccharide monooxygenases (LPMOs) are industrial enzymes which are gaining use in second generation bioethanol production from lignocellulose by acting in synergy with glycoside hydrolases. Here we present the X-ray crystal structure of an AA9 fungal LPMO from Aspergillus fumigatus and a variant which has been shown to have better performance at elevated temperatures. Based on the structures, thermal denaturation data and theoretical calculations, we provide a suggestion for the structural basis of the improved stability.

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Organizational Affiliation: 
• Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark. Electronic address: [e-mail].
Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.
Novozymes Inc, 1445 Drew Ave, CA, 95618, Davis, United States.
Novozymes A/S, Smørmosevej 25, 2880, Bagsværd, Denmark; Novo Nordisk, Diabetes Structural Biology, Novo Nordisk Park, 2760, Måløv, Denmark.

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: 48.78 kDa 
• Atom Count: 4,417 
• Modeled Residue Count: 456 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase, putative	A, B	229	Aspergillus fumigatus Af293	Mutation(s): 0  Gene Names: AFUA_4G07850 EC: 3.2.1 (PDB Primary Data), 1.14.99.56 (UniProt)
UniProt
Find proteins for Q4WP32 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WP32  Go to UniProtKB:  Q4WP32
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	C [auth A], E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT	F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.155 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.105 (Depositor), 0.105 (DCC) 
• R-Value Observed: 0.107 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.3	α = 75.86
b = 49.11	β = 88.38
c = 53.96	γ = 76.31

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
pointless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Lo Leggio, L., Poulsen, J.C.N., Weihe, C.D.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-10-17
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary