9EBK | pdb_00009ebk

Piperazate synthase (PipS) in complex with haem

• PDB DOI: https://doi.org/10.2210/pdb9EBK/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces griseus subsp. griseus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-12 Released: 2025-01-22 
• Deposition Author(s): Higgins, M.A., Ryan, K.S.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structure and mechanism of haem-dependent nitrogen-nitrogen bond formation in piperazate synthase

Higgins, M.A., Shi, X., Soler, J., Harland, J.B., Parkkila, T., Lehnert, N., Garcia-Borras, M., Du, Y.L., Ryan, K.S.

(2025) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-024-01280-8

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.63 kDa 
• Atom Count: 3,638 
• Modeled Residue Count: 438 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Piperazate synthase	A [auth B], B [auth A]	226	Streptomyces griseus subsp. griseus	Mutation(s): 0
UniProt
Find proteins for A0A7K2YFL1 (Streptomyces sp. SID3343) Explore A0A7K2YFL1  Go to UniProtKB:  A0A7K2YFL1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth B], E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.51	α = 90
b = 66.51	β = 90
c = 478.694	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Higgins, M.A., Ryan, K.S.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RPGIN-2021-02626

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release
  
• Version 1.1: 2025-02-26
  Changes: Database references