8RIO | pdb_00008rio

Beta-keto acid cleavage enzyme from Paracoccus denitrificans

• PDB DOI: https://doi.org/10.2210/pdb8RIO/pdb

• Classification: LYASE
• Organism(s): Paracoccus denitrificans PD1222
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-19 Released: 2025-01-01 
• Deposition Author(s): Marchal, D.G., Zarzycki, J., Erb, T.J.
• Funding Organization(s): Max Planck Society, European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Design and implementation of aerobic, ambient CO2-reduction as an entry-point for enhanced carbon fixation

Satanowski, A.G., Marchal, D.G., Perret, A., Petit, J.-L., Bouzon, M., Doering, V., Dubois, I., He, H., Smith, E.N., Pellouin, V., Petri, H.M., Rainaldi, V., Nattermann, M., Burgener, S., Paczia, N., Zarzycki, J., Heinemann, M., Bar-Even, A., Erb, T.J.

(null) Nat Commun 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 67.55 kDa 
• Atom Count: 5,560 
• Modelled Residue Count: 616 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-keto-5-aminohexanoate cleavage protein	A, B	310	Paracoccus denitrificans PD1222	Mutation(s): 0  Gene Names: Pden_3578
UniProt
Find proteins for A1B802 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B802  Go to UniProtKB:  A1B802

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRO	D [auth A], F [auth B]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
ZN (Subject of Investigation/LOI)	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.065	α = 90
b = 137.871	β = 90
c = 132.517	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Marchal, D.G., Zarzycki, J., Erb, T.J.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
European Commission	European Union	862087

Revision History  

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