6UCZ | pdb_00006ucz

Crystal structure of dihydropteroate synthase from Anaplasma phagocytophilum with bound 6-hydroxymethylpterin-monophosphate

• PDB DOI: https://doi.org/10.2210/pdb6UCZ/pdb

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


• Deposited: 2019-09-18 Released: 2019-10-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dihydropteroate synthase from Anaplasma phagocytophilum with bound 6-hydroxymethylpterin-monophosphate

Bolejack, M.J., Delker, S.L., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.82 kDa 
• Atom Count: 4,294 
• Modeled Residue Count: 519 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteroate synthase	A, B	292	Anaplasma phagocytophilum	Mutation(s): 0  Gene Names: WSQ_01200, folP EC: 2.5.1.15

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMM (Subject of Investigation/LOI)	C [auth A], G [auth B]	PTERIN-6-YL-METHYL-MONOPHOSPHATE C7 H8 N5 O5 P AJXFJEHKGGCFNM-UHFFFAOYSA-N
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36ucz

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.83	α = 90
b = 81.48	β = 102.67
c = 71.17	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Derived calculations
• Version 1.2: 2020-03-11
  Changes: Data collection
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description