21CL | pdb_000021cl

Co-crystal structure of 4-hydroxybenzaldehyde dehydrogenase PHBDD variant complexed with (S)-butane-1,3-diol

• PDB DOI: https://doi.org/10.2210/pdb21CL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-12-08 Released: 2026-10-28 
• Deposition Author(s): Jun, Y., Xiang, Q., Xiaoguang, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: in silico

Literature

Co-crystal structure of 4-hydroxybenzaldehyde dehydrogenase PHBDD variant complexed with (S)-butane-1,3-diol

Jun, Y., Xiang, Q., Xiaoguang, L.

To be published.

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: 225.73 kDa 
• Atom Count: 16,803 
• Modeled Residue Count: 1,950 
• Deposited Residue Count: 2,076 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxybenzaldehyde dehydrogenase (NADP(+))	A, B, C, D	519	Pseudomonas putida	Mutation(s): 0  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
BU2 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	1,3-BUTANEDIOL C4 H10 O2 PUPZLCDOIYMWBV-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.74	α = 90
b = 122.07	β = 105.66
c = 89.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Jun, Y., Xiang, Q., Xiaoguang, L.

---

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

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release