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)

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
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Ligand Structure Quality Assessment

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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

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

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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 A0ACD6BA03 (Streptomyces sp. SID3343) Explore A0ACD6BA03 Go to UniProtKB: A0ACD6BA03
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BA03
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth B] mmCIF format, chain E [auth A]	C [auth B], E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.