6PZ2 | pdb_00006pz2

Crystal Structure of FolP (dihydropteroate synthase) from Colstridium difficile in the presence of pteroic acid

• PDB DOI: https://doi.org/10.2210/pdb6PZ2/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-31 Released: 2019-11-27 
• Deposition Author(s): Girardi, N.M., Thoden, J.B., Holden, H.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.224 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of FolP (dihydropteroate synthase) from Colstridium difficile in the presence of pteroic acid

Girardi, N.M., Thoden, J.B., Holden, H.M.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.15 kDa 
• Atom Count: 2,306 
• Modeled Residue Count: 263 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteroate synthase	A	267	Clostridioides difficile	Mutation(s): 0  Gene Names: folP, SAMEA3374989_02220 EC: 2.5.1.15

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT1 (Subject of Investigation/LOI)	K [auth A]	PTEROIC ACID C14 H12 N6 O3 JOAQINSXLLMRCV-UHFFFAOYSA-N
NHE	L [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.224 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.258	α = 90
b = 156.258	β = 90
c = 84.708	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-27 
Deposition Author(s): Girardi, N.M., Thoden, J.B., Holden, H.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	gm115921

Revision History  

• Version 1.0: 2019-11-27
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description