6RM2 | pdb_00006rm2

Deoxyguanylosuccinate synthase (DgsS) structure with ATP, IMP, Magnesium

• PDB DOI: https://doi.org/10.2210/pdb6RM2/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Vibrio phage phiVC8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-04 Released: 2020-06-03 
• Deposition Author(s): Sleiman, D., Loc'h, J., Haouz, A., Kaminski, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Deoxyguanylosuccinate synthase (DgsS) quaternary structure with ATP, IMP, Magnesium at 2.5 Angstrom resolution

Sleiman, D., Loc'h, J., Haouz, A., Kaminski, P.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.74 kDa 
• Atom Count: 5,673 
• Modeled Residue Count: 686 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate synthetase	A, B	363	Vibrio phage phiVC8	Mutation(s): 0  Gene Names: phiVC8_p27 EC: 6.3.4.25
UniProt
Find proteins for G3FFN6 (Vibrio phage phiVC8) Explore G3FFN6  Go to UniProtKB:  G3FFN6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A], G [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
IMP	E [auth A], I [auth B]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
SO4	F [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	D [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.82	α = 90
b = 90.82	β = 90
c = 192.17	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Sleiman, D., Loc'h, J., Haouz, A., Kaminski, P.A.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description