8AFV

DaArgC3 - Engineered Formyl Phosphate Reductase with 3 substitutions (S178V, G182V, L233I)

• PDB DOI: https://doi.org/10.2210/pdb8AFV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Denitrovibrio acetiphilus DSM 12809
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-07-18 Released: 2023-04-05 
• Deposition Author(s): Pfister, P., Nattermann, M., Zarzycki, J., Erb, T.J.
• Funding Organization(s): German Federal Ministry for Education and Research, German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.207 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

N-acetyl-gamma-glutamyl-phosphate reductase of Denitrovibrio acetiphilus

Nattermann, M., Wenk, S., Pfister, P., Guntermann, N., Nickel, L., Zarzycki, J., Francio, G., Leitner, W., Bar-Even, A., Erb, T.J.

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 Evidence: gel filtration

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: 152.1 kDa 
• Atom Count: 10,561 
• Modelled Residue Count: 1,296 
• Deposited Residue Count: 1,368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyl-gamma-glutamyl-phosphate reductase	A, B, C, D	342	Denitrovibrio acetiphilus DSM 12809	Mutation(s): 3  Gene Names: argC, Dacet_0460 EC: 1.2.1.38
UniProt
Find proteins for D4H3H4 (Denitrovibrio acetiphilus (strain DSM 12809 / NBRC 114555 / N2460)) Explore D4H3H4  Go to UniProtKB:  D4H3H4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A], F [auth A], G [auth B], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.207 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.877	α = 90
b = 109.55	β = 90
c = 133.225	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-05 
Deposition Author(s): Pfister, P., Nattermann, M., Zarzycki, J., Erb, T.J.

---

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	031B0850B
German Research Foundation (DFG)	Germany	390919832

Revision History  

• Version 1.0: 2023-04-05
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description