9KFY | pdb_00009kfy

Crystal structure of synthetic PPR-DYW in its RNA-free state

• PDB DOI: https://doi.org/10.2210/pdb9KFY/pdb

• Classification: HYDROLASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-07 Released: 2025-11-12 
• Deposition Author(s): Aoyama, R., Gutmann, B., Ichinose, M., Yagi, Y., Nakamura, T., Kakuta, Y., Teramoto, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Models: experimental, in silico

Literature

Structural basis of C-to-U RNA editing by PPR-DYW protein

Teramoto, T., Urushihara, R., Aoyama, R., Okada, A., Gutmann, B., Ichinose, M., Yagi, Y., Kakuta, Y., Nakamura, T.

To be published.

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: 68.64 kDa 
• Atom Count: 4,861 
• Modeled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic PPR-DYW protein	A	612	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.29	α = 90
b = 94.54	β = 90
c = 101.56	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Aoyama, R., Gutmann, B., Ichinose, M., Yagi, Y., Nakamura, T., Kakuta, Y., Teramoto, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release