9GN1

Crystal structure of inactive Deacetylase (HdaH) H144A from Klebsiella pneumoniae subsp. ozaenae

• PDB DOI: https://doi.org/10.2210/pdb9GN1/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae subsp. ozaenae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-08-30 Released: 2024-11-06 
• Deposition Author(s): Qin, Q., Graf, L.G., Schulze, S., Palm, G.J., Lammers, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.204 
• R-Value Work: 0.153 

Starting Model: experimental

Literature

Distribution and diversity of classical deacylases in bacteria

Graf, L.G., Moreno-Yruela, C., Qin, C., Schulze, S., Palm, G.J., Schmoeker, O., Wang, N., Hocking, D., Jebeli, L., Girbardt, B., Berndt, L., Weis, D.M., Janetzky, M., Zuehlke, D., Sievers, S., Strugnell, R.A., Olsen, C.A., Hofmann, K., Lammers, M.

(2024) Nature Communications 

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)

Macromolecule Content

• Total Structure Weight: 41.89 kDa 
• Atom Count: 2,967 
• Modelled Residue Count: 370 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deacetylase	A	382	Klebsiella pneumoniae subsp. ozaenae	Mutation(s): 1  Gene Names: hdaH, NCTC10313_02007, NCTC5050_05964 EC: 3.5.1
UniProt
Find proteins for A0A377Z5F6 (Klebsiella pneumoniae subsp. ozaenae) Explore A0A377Z5F6  Go to UniProtKB:  A0A377Z5F6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	F [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN (Subject of Investigation/LOI)	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
K	B [auth A], C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.204 
• R-Value Work: 0.153 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.117	α = 90
b = 146.117	β = 90
c = 146.117	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Qin, Q., Graf, L.G., Schulze, S., Palm, G.J., Lammers, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	LA2984/6-1

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release