7D4L

X-ray crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+ at pH7.0

• PDB DOI: https://doi.org/10.2210/pdb7D4L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-24 Released: 2021-06-09 
• Deposition Author(s): Wan, Q., Dealwis, C.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis

Wan, Q., Bennett, B.C., Wymore, T., Li, Z., Wilson, M.A., Brooks III, C.L., Langan, P., Kovalevsky, A., Dealwis, C.G.

(2021) ACS Catal 11: 5873-5884

• DOI: https://doi.org/10.1021/acscatal.1c00417

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 19.26 kDa 
• Atom Count: 1,436 
• Modelled Residue Count: 159 
• 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 K-12	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
FOL (Subject of Investigation/LOI)	B [auth A]	FOLIC ACID C19 H19 N7 O6 OVBPIULPVIDEAO-LBPRGKRZSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.293	α = 90
b = 45.625	β = 90
c = 98.974	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Wan, Q., Dealwis, C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32071264
National Science Foundation (NSF, China)	China	31670790

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description