8DOR

Crystal structure of Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb8DOR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-14 Released: 2022-07-27 
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.162 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 

Literature

Crystal structure of Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase from Klebsiella pneumoniae

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 102.96 kDa 
• Atom Count: 8,093 
• Modelled Residue Count: 866 
• Deposited Residue Count: 900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase	A, B, C, D	225	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: nfnB, KPN_00553, KPHS_29700
UniProt
Find proteins for A6T5Y2 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T5Y2  Go to UniProtKB:  A6T5Y2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	E [auth A], I [auth B], N [auth C], S [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PO4	F [auth A], J [auth B], O [auth C], T [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], P [auth C], Q [auth C], R [auth C], U [auth D], V [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.162 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 
• Space Group: P 3₁
• Diffraction Data: https://doi.org/10.18430/M38DOR

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.826	α = 90
b = 56.826	β = 90
c = 257.568	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-22
  Changes: Data collection