8U93

Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (PEG bound)

• PDB DOI: https://doi.org/10.2210/pdb8U93/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Klebsiella aerogenes KCTC 2190
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-09-18 Released: 2023-09-27 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.202 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (PEG bound)

Lovell, S., Liu, L., Seibold, S., Battaile, K.P.

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: 34.61 kDa 
• Atom Count: 2,504 
• Modelled Residue Count: 296 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylneuraminate lyase	A	305	Klebsiella aerogenes KCTC 2190	Mutation(s): 1  Gene Names: nanA EC: 4.1.3.3
UniProt
Find proteins for A0A0H3FJT8 (Klebsiella aerogenes (strain ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56)) Explore A0A0H3FJT8  Go to UniProtKB:  A0A0H3FJT8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PG	G [auth A], H [auth A]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N
DTT	E [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI	A	L-PEPTIDE LINKING	C9 H16 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.202 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 6₂ 2 2
• Diffraction Data: https://doi.org/10.18430/m38u93

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.406	α = 90
b = 96.406	β = 90
c = 205.982	γ = 120

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: 2023-09-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection