9J0S | pdb_00009j0s

CRYSTAL STRUCTURE OF A NOVEL ALDEHYDE DEHYDROGENASE FROM KLEBSIELLA PNEUMONIAE WITH LIGAND

• PDB DOI: https://doi.org/10.2210/pdb9J0S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-08-02 Released: 2025-07-30 
• Deposition Author(s): Zhang, J., Han, Y., LIu, W.D., Zhang, W.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.260 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: in silico

Literature

Aldehyde Dehydrogenase from Klebsiella pneumoniae: A Robust Biocatalyst for Preparing Heteroatom-Containing Carboxylic Acids

Han, Y., Geng, N., Sha, J., Li, H., You, C., Liu, W., Zhang, J., Shi, J., Wu, X., Zhang, W.

(2025) Adv Synth Catal 367

• DOI: https://doi.org/10.1002/adsc.202500027

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)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 213.91 kDa 
• Atom Count: 13,700 
• Modeled Residue Count: 1,815 
• Deposited Residue Count: 1,956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase	A, B, C, D	489	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: yfmT, xylC_1, CAZ10_02010, DT376_04100, IPC1295_07430, NCTC13621_03651, PAERUG_P19_London_7_VIM_2_05_10_05035 EC: 1.2.1.3 (PDB Primary Data), 1.2.1.28 (PDB Primary Data)
UniProt
Find proteins for Q9HUR4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUR4  Go to UniProtKB:  Q9HUR4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.260 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.15	α = 90
b = 144.774	β = 90
c = 150.239	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Zhang, J., Han, Y., LIu, W.D., Zhang, W.Y.

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

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release