9NJO | pdb_00009njo

Y100F Mutant of E. coli Dihydrofolate Reductase

• PDB DOI: https://doi.org/10.2210/pdb9NJO/pdb

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


• Deposited: 2025-02-27 Released: 2025-05-28 
• Deposition Author(s): Fried, S.D.E., Mathews, I.I., Boxer, S.G.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.226 (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

Macromolecule Content 

• Total Structure Weight: 18.22 kDa 
• Atom Count: 1,376 
• Modeled Residue Count: 150 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	159	Escherichia coli	Mutation(s): 1  Gene Names: folA, tmrA, b0048, JW0047 EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12)) Explore P0ABQ4  Go to UniProtKB:  P0ABQ4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A], C [auth A], D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.85	α = 90
b = 42.65	β = 90
c = 97.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Fried, S.D.E., Mathews, I.I., Boxer, S.G.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1915727
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118044

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release