6CQG | pdb_00006cqg

YycF Effector Domain Structure without DNA bound

• PDB DOI: https://doi.org/10.2210/pdb6CQG/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-03-15 Released: 2019-06-19 
• Deposition Author(s): Riboldi-Tunnicliffe, A., Gabrielsen, M., Williamson, R.M., Panjikar, S.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

YycF Effector Domain Structure without DNA bound

Gabrielsen, M., Williamson, R.M., Panjikar, S., 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)

Macromolecule Content 

• Total Structure Weight: 11.67 kDa 
• Atom Count: 884 
• Modeled Residue Count: 98 
• Deposited Residue Count: 98 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response regulator	A	98	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: yycF, ERS021524_01324
UniProt
Find proteins for Q8DPL7 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DPL7  Go to UniProtKB:  Q8DPL7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.63	α = 90
b = 46.49	β = 90
c = 63.27	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Auto-Rickshaw	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Riboldi-Tunnicliffe, A., Gabrielsen, M., Williamson, R.M., Panjikar, S.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	QLRK2-2000-00542

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description