4ZMS | pdb_00004zms

Structure of the full-length response regulator spr1814 in complex with a phosphate analogue and B3C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.215 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

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Literature

Structural characterization of the full-length response regulator spr1814 in complex with a phosphate analogue reveals a novel conformational plasticity of the linker region

Park, A.K., Lee, J.H., Chi, Y.M., Park, H.

(2016) Biochem Biophys Res Commun 473: 625-629

  • DOI: https://doi.org/10.1016/j.bbrc.2016.03.144
  • Primary Citation Related Structures: 
    4ZMR, 4ZMS

  • PubMed Abstract: 

    Spr1814 of Streptococcus pneumoniae is a response regulator (RR) that belongs to the NarL/FixJ subfamily and has a four-helix helix-turn-helix DNA-binding domain. Here, the X-ray crystal structure of the full-length spr1814 in complex with a phosphate analogue beryllium fluoride (BeF3(-)) was determined at 2.0 Å. This allows for a structural comparison with the previously reported full-length unphosphorylated spr1814. The phosphorylation of conserved aspartic acid residue of N-terminal receiver domain triggers a structural perturbation at the α4-β5-α5 interface, leading to the domain reorganization of spr1814, and this is achieved by a rotational change in the C-terminal DNA-binding domain.

    • Organizational Affiliation: 
    • Division of Biotechnology, College of Life Sciences, Korea University, Seoul 136-713, South Korea; Division of Polar Life Sciences, Korea Polar Research Institute, Yeonsu-gu, Incheon 406-840, South Korea.

Macromolecule Content 

  • Total Structure Weight: 46.77 kDa 
  • Atom Count: 3,706 
  • Modeled Residue Count: 407 
  • Deposited Residue Count: 414 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Response regulator
A, B
207Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: rr11, spr1814
UniProt
Find proteins for Q8DNC2 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DNC2 
Go to UniProtKB:  Q8DNC2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DNC2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.215 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.98α = 90
b = 115.526β = 92.41
c = 50.073γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations