7TZP

Crystal Structure of Putataive Short-Chain Dehydrogenase/Reductase (FabG) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 in Complex with NADH

• PDB DOI:  https://doi.org/10.2210/pdb7TZP/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-02-16 Released: 2022-03-02 
• Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.

Inniss, N.L., Kochan, T.J., Minasov, G., Wawrzak, Z., Chang, C., Tan, K., Shuvalova, L., Kiryukhina, O., Pshenychnyi, S., Wu, R., Dubrovska, I., Babnigg, G., Endres, M., Anderson, W.F., Hauser, A.R., Joachimiak, A., Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0101322-e0101322

• PubMed: 36695589 
• DOI: https://doi.org/10.1128/mra.01013-22
• Primary Citation of Related Structures:  
  6DT3, 6DUX, 6DVV, 6DXN, 6E85, 6NAU, 6NBG, 6NDI, 6WN5, 6WN8, 6X1L, 7RJJ, 7TL5, 7TZP


• PubMed Abstract: 
  

Klebsiella pneumoniae is a leading cause of antibiotic-resistant-associated deaths in the world. Here, we report the deposition of 14 structures of enzymes from both the core and accessory genomes of sequence type 23 (ST23) K1 hypervirulent K. pneumoniae.

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Organizational Affiliation: 

Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 215.61 kDa 
• Atom Count: 15,486 
• Modelled Residue Count: 1,962 
• Deposited Residue Count: 1,976 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-ACP reductase	A, B, C, D, E, F, G, H	247	Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044	Mutation(s): 0  Gene Names: fabG_6, DBX64_14690, SAMEA4364603_02057 EC: 1.1.1.100
UniProt
Find proteins for A0A332H2K8 (Klebsiella pneumoniae) Explore A0A332H2K8  Go to UniProtKB:  A0A332H2K8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI (Subject of Investigation/LOI)	AA [auth C], MA [auth E], O [auth A], WA [auth G]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
GOL	AB [auth G], BA [auth C], EB [auth H], FA [auth D], NA [auth E], P [auth A], Q [auth A], R [auth A], RA [auth F], SA [auth F], V [auth B], W [auth B], XA [auth G], YA [auth G], ZA [auth G]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	BB [auth G], CA [auth C], CB [auth G], FB [auth H], GA [auth D], GB [auth H], HA [auth D], HB [auth H], OA [auth E], PA [auth E], QA [auth E], S [auth A], T [auth A], X [auth B], Y [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	I [auth A], IA [auth E], TA [auth G], U [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	DA [auth D], DB [auth H], EA [auth D], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], N [auth A], UA [auth G], VA [auth G], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.387	α = 90
b = 256.02	β = 90
c = 260.642	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references