4QI9

Crystal structure of dihydrofolate reductase from Yersinia pestis complexed with methotrexate

• PDB DOI: https://doi.org/10.2210/pdb4QI9/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-05-30 Released: 2014-07-02 
• Deposition Author(s): Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Crystal structure of dihydrofolate reductase from Yersinia pestis complexed with methotrexate

Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Shatsman, S., Anderson, W.F., Joachimiak, A.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.14 kDa 
• Atom Count: 3,966 
• Modelled Residue Count: 471 
• Deposited Residue Count: 501 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B, C	167	Yersinia pestis CO92	Mutation(s): 0  Gene Names: folA, y3688, YPO0486, YP_3693 EC: 1.5.1.3
UniProt
Find proteins for A0A3N4BLI0 (Yersinia pestis) Explore A0A3N4BLI0  Go to UniProtKB:  A0A3N4BLI0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTX	D [auth A], E [auth B], F [auth C]	METHOTREXATE C20 H22 N8 O5 FBOZXECLQNJBKD-ZDUSSCGKSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m34qi9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.196	α = 90
b = 103.641	β = 93
c = 34.288	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Structure summary