4HYE

Crystal structure of a response regulator spr1814 from Streptococcus pneumoniae reveals unique interdomain contacts among NarL family proteins

• PDB DOI: https://doi.org/10.2210/pdb4HYE/pdb

• Classification: TRANSCRIPTION ACTIVATOR
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-13 Released: 2013-06-05 
• Deposition Author(s): Park, A.K., Moon, J.H., Chi, Y.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.241 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Crystal structure of the response regulator spr1814 from Streptococcus pneumoniae reveals unique interdomain contacts among NarL family proteins.

Park, A.K., Moon, J.H., Oh, J.S., Lee, K.S., Chi, Y.M.

(2013) Biochem Biophys Res Commun 434: 65-69

• PubMed: 23545256 
• DOI: https://doi.org/10.1016/j.bbrc.2013.03.065
• Primary Citation of Related Structures:  
  4HYE


• PubMed Abstract: 
  

  Spr1814 belongs to the NarL/FixJ subfamily of signal transduction response regulators (RR), and has been predicted to regulate the neighboring ABC transporter, which translocates antibiotic molecules in Streptococcus pneumoniae. Here, we report the crystal structure of full-length unphosphorylated spr1814 at 1.7Å resolution. The asymmetric unit contains two spr1814 molecules, which display very different conformations. Through comparisons with other RRs structures, we concluded that one molecule adopts a general inactive conformation, whereas the other molecule adopts an intermediate conformation. The superposition of each molecule showed that rotational change of the effector domain occurred in intermediate conformational state, implying that domain rearrangement could occur upon phosphorylation.

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Organizational Affiliation: 

Division of Biotechnology, College of Life Sciences, Korea University, Seoul 136-713, Republic of Korea.

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)

Macromolecule Content

• Total Structure Weight: 49.2 kDa 
• Atom Count: 3,380 
• Modelled Residue Count: 400 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator	A, B	220	Streptococcus pneumoniae R6	Mutation(s): 0  Gene Names: rr11, spr1814
UniProt
Find proteins for Q8DNC2 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DNC2  Go to UniProtKB:  Q8DNC2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.241 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.91	α = 90
b = 71.376	β = 90
c = 117.727	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-05 
Deposition Author(s): Park, A.K., Moon, J.H., Chi, Y.M.

Revision History  

• Version 1.0: 2013-06-05
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references