9NI0 | pdb_00009ni0

L54A Mutant of E. coli Dihydrofolate Reductase Complexed with Nicotinamide Adenine Dinucleotide Phosphate (oxidized form)

• PDB DOI: https://doi.org/10.2210/pdb9NI0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-02-25 Released: 2025-04-23 
• Deposition Author(s): Fried, S.D.E., Boxer, S.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Role of Electrostatics in Hydride Transfer by Dihydrofolate Reductase

Fried, S.D.E., Mukherjee, S., Mao, Y., Boxer, S.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.52 kDa 
• Atom Count: 3,017 
• Modeled Residue Count: 312 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	159	Escherichia coli	Mutation(s): 1  Gene Names: folA, c0058 EC: 1.5.1.3
UniProt
Find proteins for P0ABQ5 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore P0ABQ5  Go to UniProtKB:  P0ABQ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
CA	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.597	α = 90
b = 58.812	β = 102.39
c = 71.276	γ = 90

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: 2025-04-23 
Deposition Author(s): Fried, S.D.E., Boxer, S.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118044

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release