5TGD

Crystal structure of FolM Alternative dihydrofolate reductase 1 from Brucella suis in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb5TGD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brucella suis 92/29
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-27 Released: 2016-10-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 

Starting Model: experimental

Literature

Crystal structures of FolM alternative dihydrofolate reductase 1 from Brucella suis and Brucella canis.

Porter, I., Neal, T., Walker, Z., Hayes, D., Fowler, K., Billups, N., Rhoades, A., Smith, C., Smith, K., Staker, B.L., Dranow, D.M., Mayclin, S.J., Subramanian, S., Edwards, T.E., Myler, P.J., Asojo, O.A.

(2022) Acta Crystallogr F Struct Biol Commun 78: 31-38

• PubMed: 34981773 
• DOI: https://doi.org/10.1107/S2053230X21013078
• Primary Citation of Related Structures:  
  5BT9, 5TGD


• PubMed Abstract: 
  

  Members of the bacterial genus Brucella cause brucellosis, a zoonotic disease that affects both livestock and wildlife. Brucella are category B infectious agents that can be aerosolized for biological warfare. As part of the structural genomics studies at the Seattle Structural Genomics Center for Infectious Disease (SSGCID), FolM alternative dihydrofolate reductases 1 from Brucella suis and Brucella canis were produced and their structures are reported. The enzymes share ∼95% sequence identity but have less than 33% sequence identity to other homologues with known structure. The structures are prototypical NADPH-dependent short-chain reductases that share their highest tertiary-structural similarity with protozoan pteridine reductases, which are being investigated for rational therapeutic development.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA.

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: 122.09 kDa 
• Atom Count: 8,598 
• Modelled Residue Count: 983 
• Deposited Residue Count: 1,068 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FolM Alternative dihydrofolate reductase	A, B, C, D	267	Brucella suis 92/29	Mutation(s): 0  Gene Names: C062_00524

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], H [auth B], I [auth C], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], J [auth C], L [auth D], M [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M35TGD

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.35	α = 90
b = 76.52	β = 109.47
c = 98.26	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-10-04
  Changes: Refinement description