9T01 | pdb_00009t01

Crystal structure of SarF, the ComR paralog from S.salivarius, in complex with DNA and the synthetic peptide sBI7.

• PDB DOI: https://doi.org/10.2210/pdb9T01/pdb

• Classification: TRANSCRIPTION
• Organism(s): Streptococcus salivarius, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-16 Released: 2026-10-28 
• Deposition Author(s): Nessler, S., Gallay Li de la Sierra, I.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 
  0.316 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.281 (Depositor), 0.283 (DCC) 
• R-Value Observed: 
  0.283 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of SarF, the ComR paralog from S.salivarius, in complex with DNA and the synthetic peptide sBI7.

Nessler, S., Gallay Li de la Sierra, I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 268.24 kDa 
• Atom Count: 17,398 
• Modeled Residue Count: 1,933 
• Deposited Residue Count: 2,060 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helix-turn-helix transcriptional regulator	A, B, C, D, E, F	316	Streptococcus salivarius	Mutation(s): 0  Gene Names: FHI56_08430

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
synthetic peptide sBI7	G, H [auth J], I [auth H], J [auth I]	8	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*GP*TP*GP*AP*CP*AP*TP*AP*GP*AP*TP*GP*TP*CP*CP*TP*TP*TP*T)-3')	K [auth P], L, M [auth N]	22	Streptococcus salivarius

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*GP*GP*AP*CP*AP*TP*CP*TP*AP*TP*GP*TP*CP*AP*CP*TP*TP*T)-3')	N [auth M], O, P [auth K]	22	Streptococcus salivarius

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free:  0.316 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.281 (Depositor), 0.283 (DCC) 
• R-Value Observed: 0.283 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.43	α = 90
b = 112.02	β = 106.14
c = 160.85	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Nessler, S., Gallay Li de la Sierra, I.

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Funding Organization	Location	Grant Number
Not funded	France	--

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release