9ER4

Room temperature structure of Glycine max phyA in Pr

• PDB DOI: https://doi.org/10.2210/pdb9ER4/pdb

• Classification: PLANT PROTEIN
• Organism(s): Glycine max
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-03-22 Released: 2025-01-08 
• Deposition Author(s): Nagano, S.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Structure of plant phytochrome A

Guan, K., Nagano, S., Hughes, J.

(2025) Nat Commun 

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 81.23 kDa 
• Atom Count: 5,027 
• Modelled Residue Count: 615 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytochrome A-2	A, B	359	Glycine max	Mutation(s): 0  Gene Names: PHYA2, GLYMA_20G090000
UniProt
Find proteins for B4YB07 (Glycine max) Explore B4YB07  Go to UniProtKB:  B4YB07

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC (Subject of Investigation/LOI)	C [auth A], D [auth B]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.45	α = 90
b = 115.05	β = 92.68
c = 69.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-08 
Deposition Author(s): Nagano, S.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB1078

Revision History  

• Version 1.0: 2025-01-08
  Type: Initial release