7TMG | pdb_00007tmg

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 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of NAD(P)H nitroreductases from Klebsiella pneumoniae

Kancherla, A.D., Liu, L., Tillery, L., Shek, R., Craig, J.K., Machen, A.J., Seibold, S., Battaile, K.P., Fradi, S., Barrett, L.K., Subramanian, S., Myler, P., Van Voorhis, W.C., Lovell, S.

(2024) Acta Crystallogr F Struct Biol Commun F80: 173-182

• DOI: https://doi.org/10.1107/S2053230X24006472

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 
• Modeled 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 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37TMG

Space Group: P 2₁ 2₁ 2

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
• Version 1.2: 2024-08-14
  Changes: Database references