9DH4 | pdb_00009dh4

Crystal structure of PIsnA complexed with L-Tyrosine

• PDB DOI: https://doi.org/10.2210/pdb9DH4/pdb

• Classification: TRANSFERASE
• Organism(s): Photorhabdus luminescens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-03 Released: 2025-07-16 
• Deposition Author(s): Kim, W., Zhang, Y.J., Guo, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

Studies of Isonitrile Synthases Help Elucidate the Mechanism of Isonitrile Installation

Chen, T.Y., Kim, W., Guo, M., Yao, A., Zhang, Y.J., Chang, W.C.

(2025) ACS Catal : 12005-12013

• DOI: https://doi.org/10.1021/acscatal.5c03282

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.8 kDa 
• Atom Count: 5,078 
• Modeled Residue Count: 624 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-tyrosine/L-tryptophan isonitrile synthase family protein	A, B	315	Photorhabdus luminescens	Mutation(s): 0  Gene Names: GPY51_01455
UniProt
Find proteins for A0A1G5Q840 (Photorhabdus luminescens) Explore A0A1G5Q840  Go to UniProtKB:  A0A1G5Q840

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYR (Subject of Investigation/LOI)	D [auth A], F [auth B]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
PO4 (Subject of Investigation/LOI)	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.452	α = 90
b = 133.452	β = 90
c = 110.283	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Kim, W., Zhang, Y.J., Guo, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM148356

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release