6STX | pdb_00006stx

Copper oxidase from Colletotrichum graminicola

• PDB DOI: https://doi.org/10.2210/pdb6STX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Colletotrichum graminicola M1.001
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2019-09-12 Released: 2019-11-13 
• Deposition Author(s): Offen, W.A., Henrissat, B., Davies, G.J.
• Funding Organization(s): Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.219 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Discovery of a Fungal Copper Radical Oxidase with High Catalytic Efficiency toward 5-Hydroxymethylfurfural and Benzyl Alcohols for Bioprocessing

Mathieu, Y., Viborg, A.H., Forget, S.M., Brumer, H., Ciano, L., Offen, W.A., Blagova, E., Walton, P.H., Davies, G.J.

(2020) ACS Catal 

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: 78.07 kDa 
• Atom Count: 5,363 
• Modeled Residue Count: 663 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch domain-containing protein	A [auth C]	714	Colletotrichum graminicola M1.001	Mutation(s): 0  Gene Names: GLRG_02805 EC: 1.1.3.7
UniProt
Find proteins for E3Q9X3 (Colletotrichum graminicola (strain M1.001 / M2 / FGSC 10212)) Explore E3Q9X3  Go to UniProtKB:  E3Q9X3
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	B [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ACT	C	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	E [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.219 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.327	α = 90
b = 172.327	β = 90
c = 172.327	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Offen, W.A., Henrissat, B., Davies, G.J.

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Funding Organization	Location	Grant Number
Royal Society	United Kingdom	RP150126

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2020-03-18
  Changes: Advisory, Data collection, Derived calculations, Refinement description
• Version 1.2: 2020-05-27
  Changes: Database references, Structure summary
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-11-13
  Changes: Structure summary