9GLB

Crystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae

• PDB DOI: https://doi.org/10.2210/pdb9GLB/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae subsp. ozaenae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-27 Released: 2024-11-06 
• Deposition Author(s): Qin, C., 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: 2.10 Å
• R-Value Free: 0.181 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 41.95 kDa 
• Atom Count: 3,071 
• 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 [auth C]	382	Klebsiella pneumoniae subsp. ozaenae	Mutation(s): 0  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
GOL	B [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	C	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
K	D [auth C], E [auth C], F [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.181 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.163	α = 90
b = 147.163	β = 90
c = 147.163	γ = 90

Software Package:

Software Name	Purpose
PHENIX	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, C., 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