6ZAK | pdb_00006zak

Room temperature XFEL Isopenicillin N synthase structure in complex with the Fe(IV)=O mimic VO and ACV.

• PDB DOI: https://doi.org/10.2210/pdb6ZAK/pdb

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


• Deposited: 2020-06-05 Released: 2022-01-12 
• Deposition Author(s): Rabe, P., Kamps, J.J.A.G., Sutherlin, K., Pharm, C., McDonough, M.A., Leissing, T.M., Aller, P., Butryn, A., Linyard, J., Lang, P., Brem, J., Fuller, F.D., Batyuk, A., Hunter, M.S., Pettinati, I., Clifton, I.J., Alonso-Mori, R., Gul, S., Young, I., Kim, I., Bhowmick, A., ORiordan, L., Brewster, A.S., Claridge, T.D.W., Sauter, N.K., Yachandra, V., Yano, J., Kern, J.F., Orville, A.M., Schofield, C.J.
• Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom), Royal Society, Biotechnology and Biological Sciences Research Council (BBSRC), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.226 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Unanticipated intermediates during isopenicillin N synthase catalysis identified by time-resolved X-ray free-electron laser studies

Rabe, P., Makita, H., Southwart, R., Thomas, M.G., Kazaks, M., Basak, S., Zhou, T., Myers, W.K., Doyle, M.D., Simon, P.S., Hayama, S., Mosselmans, J.F.W., Stead, A.T., Oluwole, A.O., Sami, M., Clifton, I., Aller, P., Bhowmick, A., Tumber, A., Kamps, J.J.A.G., Calvopina, K., Butryn, A., Bosman, R., Cheema, A., Welsh, J., Linyard, J.D.S., Foster, F.J.H., Lang, P.A., de Munnik, M., Keable, S.M., Dasgupta, M., Kim, I.S., Bogacz, I., Chatterjee, K., Sutherlin, K.D., Kaminsky, C.J., Brem, J., McDonough, M.A., Redfield, C., Montgomery, J.R.D., Mycroft, C., Shilova, A., Devenish, N., Poitevin, F.P., Dehe, S., Tiwari, V., Sanchez, H., Rosenberg, D.J., Hunter, M.S., Gee, L.B., Bergmann, U., Alonso-Mori, R., Park, J., Owada, S., Tono, K., Axford, D., Owen, R.L., Paley, D.W., Sauter, N.K., Mittan-Moreau, D., Brewster, A.S., Robinson, C.V., Yachandra, V.K., Yano, J., Suna, E., Christov, C.Z., Orville, A.M., Kern, J.F., Schofield, C.J.

(2026) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-026-01618-4

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: 38.09 kDa 
• Atom Count: 2,858 
• 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)	C [auth A]	L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE C14 H25 N3 O6 S BYEIJZFKOAXBBV-ATZCPNFKSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
VVO (Subject of Investigation/LOI)	D [auth A]	oxovanadium(2+) O V MHHDXUNFNAZUGB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.226 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.79	α = 90
b = 75.564	β = 90
c = 101.724	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Rabe, P., Kamps, J.J.A.G., Sutherlin, K., Pharm, C., McDonough, M.A., Leissing, T.M., Aller, P., Butryn, A., Linyard, J., Lang, P., Brem, J., Fuller, F.D., Batyuk, A., Hunter, M.S., Pettinati, I., Clifton, I.J., Alonso-Mori, R., Gul, S., Young, I., Kim, I., Bhowmick, A., ORiordan, L., Brewster, A.S., Claridge, T.D.W., Sauter, N.K., Yachandra, V., Yano, J., Kern, J.F., Orville, A.M., Schofield, C.J.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106244/Z/14/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	106244/Z/14/Z
Wellcome Trust	United Kingdom	210734/Z/18/Z
Royal Society	United Kingdom	RSWF/R2/182017
Wellcome Trust	United Kingdom	102593
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	102593
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/S50676X/1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM133081
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	GM110501
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM126289
Department of Energy (DOE, United States)	United States	DOE BES DE-AC02-05CH11231
Department of Energy (DOE, United States)	United States	DOE BES DE-AC02-76SF00515

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Refinement description
• Version 2.0: 2026-09-02
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2026-10-21
  Changes: Database references