9RCO | pdb_00009rco

1,2-propanediol dehydratase with 0.1 % glycerol additive

• PDB DOI: https://doi.org/10.2210/pdb9RCO/pdb

• Classification: LYASE
• Organism(s): Raoultella planticola
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-29 Released: 2025-06-11 
• Deposition Author(s): Kalnins, G., Estere, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: in silico

Literature

1,2-propanediol dehydratase with 0.1 % glycerol additive

Kalnins, G., Estere, M.

To be published.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 366.71 kDa 
• Atom Count: 27,369 
• Modeled Residue Count: 3,172 
• Deposited Residue Count: 3,264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycyl radical protein	A, B, C, D	816	Raoultella planticola	Mutation(s): 0  Gene Names: I8Y23_000693
UniProt
Find proteins for A0AAN5KVK2 (Raoultella planticola) Explore A0AAN5KVK2  Go to UniProtKB:  A0AAN5KVK2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	H [auth C], J [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], I [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.529	α = 90
b = 199.413	β = 107.023
c = 118.1	γ = 90

Software Package:

Software Name	Purpose
xia2	data reduction
PHENIX	refinement
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Kalnins, G., Estere, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release