8F09 | pdb_00008f09

Crystal structure of a trimethoprim-resistant dihydrofolate reductase (DHFR) enzyme from an uncultured soil bacterium

• PDB DOI: https://doi.org/10.2210/pdb8F09/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-02 Released: 2022-11-16 
• Deposition Author(s): Stogios, P.J., Evdokimova, D., Borek, D., Di Leo, R., Semper, C., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.349 (Depositor), 0.352 (DCC) 
• R-Value Work: 
  0.289 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.292 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a trimethoprim-resistant dihydrofolate reductase (DHFR) enzyme from an uncultured soil bacterium

Stogios, P.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.93 kDa 
• Atom Count: 2,807 
• Modeled Residue Count: 334 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	167	uncultured bacterium	Mutation(s): 0  EC: 1.5.1.3
UniProt
Find proteins for A0A8A1VA22 (uncultured organism) Explore A0A8A1VA22  Go to UniProtKB:  A0A8A1VA22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.349 (Depositor), 0.352 (DCC) 
• R-Value Work:  0.289 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.292 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.073	α = 82
b = 41.987	β = 90
c = 70.38	γ = 72.1

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing
Coot	model building
PHENIX	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Stogios, P.J., Evdokimova, D., Borek, D., Di Leo, R., Semper, C., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2023-01-25
  Changes: Other, Structure summary
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description