8RDB

Isopenicillin N synthase N252E variant in complex with Fe and ACV under anaerobic conditions

• PDB DOI: https://doi.org/10.2210/pdb8RDB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus nidulans FGSC A4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-12-07 Released: 2024-12-18 
• Deposition Author(s): Stead, A., Rabe, P., Schofield, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.193 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Starting Model: experimental

Literature

Isopenicillin N synthase N252E variant in complex with Fe and ACV under anaerobic conditions

Stead, A., Rabe, P., Schofield, C.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.38 kDa 
• Atom Count: 3,126 
• Modelled Residue Count: 329 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isopenicillin N synthase	A	331	Aspergillus nidulans FGSC A4	Mutation(s): 1  Gene Names: ipnA, ips, AN2622 EC: 1.21.3.1
UniProt
Find proteins for P05326 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore P05326  Go to UniProtKB:  P05326

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACV (Subject of Investigation/LOI)	G [auth A]	L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE C14 H25 N3 O6 S BYEIJZFKOAXBBV-ATZCPNFKSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE (Subject of Investigation/LOI)	F [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.193 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.27	α = 90
b = 74.56	β = 90
c = 101.07	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Stead, A., Rabe, P., Schofield, C.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V001892/1
Wellcome Trust	United Kingdom	227298/Z/23/Z

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release