5HI6 | pdb_00005hi6

The high resolution structure of dihydrofolate reductase from Yersinia pestis complex with methotrexate as closed form

• PDB DOI: https://doi.org/10.2210/pdb5HI6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-11 Released: 2016-02-03 
• Deposition Author(s): Chang, C., Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Papazisi, L., 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: 2.05 Å
• R-Value Free: 
  0.223 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

The high resolution structure of dihydrofolate reductase from Yersinia pestis complex with methotrexate as closed form

Chang, C., Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 38.46 kDa 
• Atom Count: 2,922 
• Modeled Residue Count: 323 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	163	Yersinia pestis CO92	Mutation(s): 0  Gene Names: folA, AK38_2080 EC: 1.5.1.3
UniProt
Find proteins for A0A3N4BLI0 (Yersinia pestis) Explore A0A3N4BLI0  Go to UniProtKB:  A0A3N4BLI0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTX	C [auth A], F [auth B]	METHOTREXATE C20 H22 N8 O5 FBOZXECLQNJBKD-ZDUSSCGKSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	E [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.223 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35hi6

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.151	α = 90
b = 60.623	β = 90
c = 109.942	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
SBC-Collect	data collection
Coot	model building
HKL-3000	phasing
BUCCANEER	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Chang, C., Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2016-02-10
  Changes: Database references, Structure summary
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection, Database references
• Version 1.5: 2024-10-30
  Changes: Structure summary