6CXM | pdb_00006cxm

Crystal structure of a dihydrofolate reductase from Mycobacterium smegmatis in complex with NADP and P218

• PDB DOI: https://doi.org/10.2210/pdb6CXM/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-03 Released: 2018-04-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a dihydrofolate reductase from Mycobacterium smegmatis in complex with NADP and P218

Edwards, T.E., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Seattle Structural Genomics Center for Infectious Disease

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.15 kDa 
• Atom Count: 2,567 
• Modeled Residue Count: 310 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	164	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: folA, MSMEI_2607 EC: 1.5.1.3
UniProt
Find proteins for I7FC10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7FC10  Go to UniProtKB:  I7FC10

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MMV	D [auth A], F [auth B]	3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid C18 H24 N4 O4 VDGXZSSDCDPCRF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36CXM

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.25	α = 90
b = 40.3	β = 93.86
c = 67.22	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description