5VK4 | pdb_00005vk4

Crystal structure of a phosphoribosylformylglycinamidine cyclo-ligase from Neisseria gonorrhoeae bound to AMPPNP and magnesium

• PDB DOI: https://doi.org/10.2210/pdb5VK4/pdb

• Classification: LIGASE
• Organism(s): Neisseria gonorrhoeae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-20 Released: 2017-05-10 
• 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: 
  0.244 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a phosphoribosylformylglycinamidine cyclo-ligase from Neisseria gonorrhoeae bound to AMPPNP and magnesium

Edwards, T.E., Abendroth, J., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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: 77.03 kDa 
• Atom Count: 4,842 
• Modeled Residue Count: 654 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylformylglycinamidine cyclo-ligase	A, B	352	Neisseria gonorrhoeae	Mutation(s): 0  Gene Names: purM, WHOG_01214C, WHOG_02062, WHON_01216C, WHON_01605, WHOO_01146C, WHOO_02090 EC: 6.3.3.1
UniProt
Find proteins for Q5F973 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F973  Go to UniProtKB:  Q5F973

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A], E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.244 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.25	α = 90
b = 79.61	β = 90
c = 150.07	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description