5CVI | pdb_00005cvi

Structure of the manganese regulator SloR

• PDB DOI: https://doi.org/10.2210/pdb5CVI/pdb

• Classification: Transcription regulator
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-27 Released: 2015-08-12 
• Deposition Author(s): Nye, D., Glasfeld, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.258 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

SloR structure and DNA binding studies inform the SloR-SRE interaction in Streptococcus mutans

Spatafora, G., Corbett, J., Cornacchione, L.P., Daly, W.C., Galan-Donlo, D., Wysota, M., Tivnan, P., Collins, J., Nye, D., Levitz, T., Breyer, W.A., Glasfeld, 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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.91 kDa 
• Atom Count: 3,519 
• Modeled Residue Count: 427 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SloR	A, B	215	Streptococcus mutans	Mutation(s): 0  Gene Names: sloR
UniProt
Find proteins for Q9KIJ2 (Streptococcus mutans) Explore Q9KIJ2  Go to UniProtKB:  Q9KIJ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.258 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.432	α = 90
b = 60.432	β = 90
c = 298.78	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Nye, D., Glasfeld, A.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2020-02-26
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary