8WJD

Structure of SptTad2 complexed with cGG

• PDB DOI: https://doi.org/10.2210/pdb8WJD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Sphingobacterium thalpophilum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-25 Released: 2024-09-25 
• Deposition Author(s): Xiao, Y., Feng, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.237 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Starting Model: in silico

Literature

Structure of SptTad2 complexed with cGG

Xiao, Y., Feng, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 12.29 kDa 
• Atom Count: 906 
• Modelled Residue Count: 101 
• Deposited Residue Count: 101 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SptTad2	A	101	Sphingobacterium thalpophilum	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E (Subject of Investigation/LOI)	B [auth A]	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.237 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.55	α = 90
b = 61.55	β = 90
c = 97.51	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Xiao, Y., Feng, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release