6FM3

Deoxyguanylosuccinate synthase (DgsS) structure with ADP at 1.9 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6FM3/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Vibrio phage phiVC8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-01-30 Released: 2019-06-12 
• 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: 1.95 Å
• R-Value Free: 0.252 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

Deoxyguanylosuccinate synthase (DgsS) quaternary structure with ATP0, dGMP, Magnesium at 2.3 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 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.86 kDa 
• Atom Count: 2,742 
• Modelled Residue Count: 304 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.252 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.78	α = 90
b = 58.2	β = 102.44
c = 71.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Sleiman, D., Loc'h, J., Haouz, A., Kaminski, P.A.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release