3SFM | pdb_00003sfm

Novel crystallization conditions for tandem variant R67 DHFR yields wild-type crystal structure

• PDB DOI: https://doi.org/10.2210/pdb3SFM/pdb

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


• Deposited: 2011-06-13 Released: 2011-11-02 
• Deposition Author(s): Yachnin, B.J., Berghuis, A.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.164 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Novel crystallization conditions for tandem variant R67 DHFR yield a wild-type crystal structure.

Yachnin, B.J., Colin, D.Y., Volpato, J.P., Ebert, M., Pelletier, J.N., Berghuis, A.M.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1316-1322

• PubMed: 22102224 
• DOI: https://doi.org/10.1107/S1744309111030417
• Primary Citation Related Structures: 
  3SFM


• PubMed Abstract: 
  

  Trimethoprim is an antibiotic that targets bacterial dihydrofolate reductase (DHFR). A plasmid-encoded DHFR known as R67 DHFR provides resistance to trimethoprim in bacteria. To better understand the mechanism of this homotetrameric enzyme, a tandem dimer construct was created that linked two monomeric R67 DHFR subunits together and mutated the sequence of residues 66-69 of the first subunit from VQIY to INSF. Using a modified crystallization protocol for this enzyme that included in situ proteolysis using chymotrypsin, the tandem dimer was crystallized and the structure was solved at 1.4 Å resolution. Surprisingly, only wild-type protomers were incorporated into the crystal. Further experiments demonstrated that the variant protomer was selectively degraded by chymotrypsin, although no canonical chymotrypsin cleavage site had been introduced by these mutations.

---

Organizational Affiliation: 
• Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Bellini Pavilion, Room 470, Montreal, Quebec H3G 0B1, Canada.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 7.09 kDa 
• Atom Count: 567 
• Modeled Residue Count: 58 
• Deposited Residue Count: 62 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase type 2	A	62	Escherichia coli	Mutation(s): 1  Gene Names: dfrB EC: 1.5.1.3
UniProt
Find proteins for P00383 (Escherichia coli) Explore P00383  Go to UniProtKB:  P00383

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	B [auth A], C [auth A], D [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.164 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.691	α = 90
b = 67.691	β = 90
c = 51.76	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Yachnin, B.J., Berghuis, A.M.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2011-12-07
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description