6EB7 | pdb_00006eb7

YycF homologue (SP1227) Receiver Domain Activated by BeF3

• PDB DOI: https://doi.org/10.2210/pdb6EB7/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-05 Released: 2019-11-13 
• Deposition Author(s): Riboldi-Tunnicliffe, A., Issacs, N.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

YycF homologue (SP1227) Receiver Domain Activated by BeF3

Riboldi-Tunnicliffe, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 13.38 kDa 
• Atom Count: 1,048 
• Modeled Residue Count: 117 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response regulator	A	117	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: SP_1227
UniProt
Find proteins for A0A0H2UQ68 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UQ68  Go to UniProtKB:  A0A0H2UQ68

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEF	B [auth A]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.563	α = 90
b = 93.324	β = 90
c = 37.456	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Riboldi-Tunnicliffe, A., Issacs, N.W.

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Advisory, Database references
• Version 1.2: 2024-05-22
  Changes: Data collection