8SZD

Crystal structure of Yersinia pestis dihydrofolate reductase at 1.25-A resolution

• PDB DOI: https://doi.org/10.2210/pdb8SZD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-29 Released: 2023-06-07 
• Deposition Author(s): Shaw, G.X., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.221 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Crystal structure of Yersinia pestis dihydrofolate reductase at 1.25-A resolution

Shaw, G.X., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.59 kDa 
• Atom Count: 1,587 
• Modelled Residue Count: 161 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	164	Yersinia pestis	Mutation(s): 0  Gene Names: folA, tmrA, YPO0486 EC: 1.5.1.3
UniProt
Find proteins for A0A3N4BLI0 (Yersinia pestis) Explore A0A3N4BLI0  Go to UniProtKB:  A0A3N4BLI0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.221 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.257	α = 90
b = 79.156	β = 90
c = 64.347	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
DENZO	data reduction
AMoRE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Shaw, G.X., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection