8Q2M

18mer DNA mimic Foldamer with an Aliphatic linker in complex with Sac7d V26A/M29A protein

• PDB DOI: https://doi.org/10.2210/pdb8Q2M/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Sulfolobus acidocaldarius, synthetic construct
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-08-02 Released: 2023-08-23 
• Deposition Author(s): Deepak, D., Corvaglia, V., Wu, J., Huc, I.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 0.335 
• R-Value Work: 0.325 
• R-Value Observed: 0.326 

Literature

18mer DNA mimic foldamer with Alphatic linker in complex with Sac7d wild protein.

Deepak, D., Corvaglia, V., Wu, J., Huc, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 12.61 kDa 
• Atom Count: 820 
• Modelled Residue Count: 83 
• Deposited Residue Count: 86 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein 7b	A [auth AA]	66	Sulfolobus acidocaldarius	Mutation(s): 0  Gene Names: Saci_0064
UniProt
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore P13123  Go to UniProtKB:  P13123

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA mimic Foldamer	B [auth A], C [auth B]	10	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
V4F	B [auth A], C [auth B]	PEPTIDE LINKING	C12 H13 N2 O6 P		V4F
V53	B [auth A], C [auth B]	PEPTIDE LINKING	C11 H11 N2 O6 P		ES1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 0.335 
• R-Value Work: 0.325 
• R-Value Observed: 0.326 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.92	α = 90
b = 70.92	β = 90
c = 119.29	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Deepak, D., Corvaglia, V., Wu, J., Huc, I.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Derived calculations