6K0E | pdb_00006k0e

The quinary complex of AsqJ-Fe-2OG-dehydrocyclopeptin-dioxygen

• PDB DOI: https://doi.org/10.2210/pdb6K0E/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus nidulans FGSC A4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-06 Released: 2020-03-18 
• Deposition Author(s): Liao, H.J., Chan, N.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

The quinary complex of AsqJ-Fe-2OG-dehydrocyclopeptin-dioxygen

Liao, H.J., Chan, N.L.

(2020) J Am Chem Soc 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.62 kDa 
• Atom Count: 2,474 
• Modeled Residue Count: 287 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron/alpha-ketoglutarate-dependent dioxygenase asqJ	A [auth B]	327	Aspergillus nidulans FGSC A4	Mutation(s): 0  Gene Names: asqJ, AN9227 EC: 1.14 (PDB Primary Data), 1.14.11.81 (UniProt)
UniProt
Find proteins for Q5AR53 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore Q5AR53  Go to UniProtKB:  Q5AR53

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO0 (Subject of Investigation/LOI)	D [auth B]	(3~{Z})-4-methyl-3-(phenylmethylidene)-1~{H}-1,4-benzodiazepine-2,5-dione C17 H14 N2 O2 FYVKHLSOIIPVEH-PTNGSMBKSA-N
AKG	C [auth B]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE	B	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
PEO	E [auth B]	HYDROGEN PEROXIDE H2 O2 MHAJPDPJQMAIIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.805	α = 90
b = 119.638	β = 90
c = 67.198	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Liao, H.J., Chan, N.L.

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description