9PXC | pdb_00009pxc

Y100F Mutant of E. coli Dihydrofolate Reductase Complexed with NADP+ (oxidized form)

• PDB DOI: https://doi.org/10.2210/pdb9PXC/pdb

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


• Deposited: 2025-08-05 Released: 2025-09-03 
• Deposition Author(s): Fried, S.D.E., Mathews, I.I., 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: 2.37 Å
• R-Value Free: 
  0.262 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Role of Electrostatics in Hydride Transfer by Dihydrofolate Reductase

Fried, S.D.E., Mukherjee, S., 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: 18.79 kDa 
• Atom Count: 1,306 
• Modeled Residue Count: 155 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.262 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.326	α = 90
b = 57.425	β = 90
c = 73.992	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Fried, S.D.E., Mathews, I.I., 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: 2025-09-03
  Type: Initial release