8PY6 | pdb_00008py6

Isopenicillin N synthase in complex with Fe and ACdV under anaerobic conditions

• PDB DOI: https://doi.org/10.2210/pdb8PY6/pdb

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


• Deposited: 2023-07-25 Released: 2024-08-07 
• Deposition Author(s): Rabe, P., Schofield, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Isopenicillin N synthase in complex with Fe and ACdV under anaerobic conditions

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.18 kDa 
• Atom Count: 2,900 
• Modeled Residue Count: 328 
• 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): 0  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)	E [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]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.552	α = 90
b = 75.593	β = 90
c = 101.689	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
cctbx.xfel.merge	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): 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	210734/Z/18/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V001892/1
Department of Energy (DOE, United States)	United States	DE- AC02-76SF00515
Department of Energy (DOE, United States)	United States	DE-AC02- 05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM117126
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM55302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM110501
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM126289
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1P41GM139687
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10 OD023453

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release