9JVL | pdb_00009jvl

Co-crystal structure of PHBDD-M1-L163G-T234A with N-cyclopropyl-4-methylbenzamide

• PDB DOI: https://doi.org/10.2210/pdb9JVL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-10-09 Released: 2026-01-14 
• Deposition Author(s): Yang, J., Gao, L., Qiu, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

Literature

Engineered aldehyde dehydrogenases for amide bond formation

Gao, L., Qiu, X., Yang, J., Hu, K., Li, P., Li, W., Gao, F., Gallou, F., Kleinbeck, F., Lei, X.

(2026) Science 

• DOI: https://doi.org/10.1126/science.adw3365

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 213.63 kDa 
• Atom Count: 15,838 
• Modeled Residue Count: 1,947 
• Deposited Residue Count: 1,972 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxybenzaldehyde dehydrogenase (NADP(+))	A, B, C, D	493	Pseudomonas putida	Mutation(s): 2  Gene Names: pchA EC: 1.2.1.96
UniProt
Find proteins for Q59702 (Pseudomonas putida) Explore Q59702  Go to UniProtKB:  Q59702

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EDB	E [auth A], F [auth B], G [auth C], H [auth D]	~{N}-cyclopropyl-4-methyl-benzamide C11 H13 N O BRCUSPLHYFOGLC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.254	α = 90
b = 124.895	β = 105.69
c = 90.678	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHENIX	phasing
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-14 
Deposition Author(s): Yang, J., Gao, L., Qiu, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-01-14
  Type: Initial release