8D5G | pdb_00008d5g

Crystal structure of dihydropteroate synthase (folP-SMZ_B27) from soil uncultured bacterium in complex with 6-hydroxymethyl-7,8-dihydropterin pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb8D5G/pdb

• Classification: TRANSFERASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-04 Released: 2022-06-15 
• Deposition Author(s): Stogios, P.J., Skarina, T., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dihydropteroate synthase (folP-SMZ_B27) from soil uncultured bacterium in complex with 6-hydroxymethyl-7,8-dihydropterin pyrophosphate

Stogios, P.J.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.87 kDa 
• Atom Count: 4,318 
• Modeled Residue Count: 545 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
folP-SMZ_B27	A, B	273	uncultured bacterium	Mutation(s): 0  Gene Names: folP-SMZ_B27

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HH2 (Subject of Investigation/LOI)	C [auth A], G [auth B]	6-HYDROXYMETHYLPTERIN-DIPHOSPHATE C7 H9 N5 O8 P2 AMDUVUKDRBIVAH-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.54	α = 90
b = 101.54	β = 90
c = 207.009	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Stogios, P.J., Skarina, T., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description