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)

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
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HUR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.