5M0T | pdb_00005m0t

Alpha-ketoglutarate-dependent non-heme iron oxygenase EasH

• PDB DOI: https://doi.org/10.2210/pdb5M0T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus japonicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-05 Released: 2016-12-07 
• Deposition Author(s): Jakubczyk, D., Caputi, L., Stevenson, C.E.M., Lawson, D.M., O'Connor, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.244 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of EasH (Aspergillus japonicus) - an oxidase involved in cycloclavine biosynthesis.

Jakubczyk, D., Caputi, L., Stevenson, C.E., Lawson, D.M., O'Connor, S.E.

(2016) Chem Commun (Camb) 52: 14306-14309

• PubMed: 27885368 
• DOI: https://doi.org/10.1039/c6cc08438a
• Primary Citation Related Structures: 
  5M0T


• PubMed Abstract: 
  

  Aj_EasH is a non-heme iron- and α-keto-glutarate-dependent oxidase that is responsible for an unusual cyclopropyl ring formation in the biosynthesis of the fungal ergot alkaloid cycloclavine. The three dimensional structure of Aj_EasH (2.2 Å resolution) reported here provides insight into the mechanism of this unusual and complex reaction.

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Organizational Affiliation: 
• Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 65.99 kDa 
• Atom Count: 4,551 
• Modeled Residue Count: 566 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent non-heme iron oxygenase EasH	A, B	294	Aspergillus japonicus	Mutation(s): 0
UniProt
Find proteins for A0A1L1QK38 (Aspergillus japonicus) Explore A0A1L1QK38  Go to UniProtKB:  A0A1L1QK38

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	D [auth A], H [auth A], J [auth B]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], G [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE2	C [auth A], I [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.244 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.25	α = 90
b = 100.17	β = 90
c = 148.88	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Jakubczyk, D., Caputi, L., Stevenson, C.E.M., Lawson, D.M., O'Connor, S.E.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description