2A9R | pdb_00002a9r

RR02-Rec Phosphate in the active site

• PDB DOI: https://doi.org/10.2210/pdb2A9R/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-07-12 Released: 2006-09-26 
• Deposition Author(s): Riboldi-Tunnicliffe, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.246 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of an activated YycF homologue, the essential response regulator from S. pneumoniae in complex with BeF3 and the effect of pH on BeF3 binding, possible phosphate in the active site

Riboldi-Tunnicliffe, 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.

Macromolecule Content 

• Total Structure Weight: 13.84 kDa 
• Atom Count: 956 
• Modeled Residue Count: 118 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response regulator	A	120	Streptococcus pneumoniae TIGR4	Mutation(s): 1
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
XE	C [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHD	A	L-PEPTIDE LINKING	C4 H8 N O7 P		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.246 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.673	α = 90
b = 92.829	β = 90
c = 36.789	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-26 
Deposition Author(s): Riboldi-Tunnicliffe, A.

Revision History  

• Version 1.0: 2006-09-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description