7TMG

Crystal Structure of NAD(P)H nitroreductase from Klebsiella pneumoniae (long b-axis)

• PDB DOI: https://doi.org/10.2210/pdb7TMG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-19 Released: 2022-02-02 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Literature

Crystal Structure of NAD(P)H nitroreductase from Klebsiella pneumoniae (long b-axis)

Machen, A.J., Liu, L., Lovell, S., Battaile, K.P., Tillery, L., Shek, R., Craig, J.K., Barrett, L.K., Van Voorhis, W.C.

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

Macromolecule Content

• Total Structure Weight: 43.88 kDa 
• Atom Count: 3,123 
• Modelled Residue Count: 366 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H nitroreductase	A, B	191	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0  Gene Names: ydjA, E3U37_20475, E3U38_02825, E9161_16570, NCTC9504_03979 EC: 1
UniProt
Find proteins for A0A0H3GLR2 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GLR2  Go to UniProtKB:  A0A0H3GLR2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PO4	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M37TMG

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.577	α = 90
b = 99.965	β = 90
c = 63.864	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
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

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description