6DEB | pdb_00006deb

Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase in the Complex with Methotrexate from Campylobacter jejuni

• PDB DOI: https://doi.org/10.2210/pdb6DEB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-11 Released: 2018-05-23 
• Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Maltseva, N., Grimshaw, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase in the Complex with Methotrexate from Campylobacter jejuni

Kim, Y., Makowska-Grzyska, M., Maltseva, N., Grimshaw, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 63.26 kDa 
• Atom Count: 5,076 
• Modeled Residue Count: 568 
• Deposited Residue Count: 570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein FolD	A, B	285	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0  Gene Names: folD, Cj0855 EC: 1.5.1.5 (PDB Primary Data), 3.5.4.9 (PDB Primary Data)
UniProt
Find proteins for Q0PA35 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0PA35  Go to UniProtKB:  Q0PA35

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTX	J [auth B], K [auth B]	METHOTREXATE C20 H22 N8 O5 FBOZXECLQNJBKD-ZDUSSCGKSA-N
DTT	N [auth B]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
GUN	C [auth A]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N
TRS	I [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	E [auth A], G [auth A], H [auth A], M [auth B], P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	F [auth A], L [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.867	α = 90
b = 59.086	β = 100.08
c = 72.993	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Maltseva, N., Grimshaw, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

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

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description