2FTK

berylloflouride Spo0F complex with Spo0B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of Beryllofluoride Spo0F in Complex with the Phosphotransferase Spo0B Represents a Phosphotransfer Pretransition State.

Varughese, K.I.Tsigelny, I.Zhao, H.

(2006) J.Bacteriol. 188: 4970-4977

  • DOI: 10.1128/JB.00160-06

  • PubMed Abstract: 
  • A number of regulatory circuits in biological systems function through the exchange of phosphoryl groups from one protein to another. Spo0F and Spo0B are components of a phosphorelay that control sporulation in the bacterium Bacillus subtilis through ...

    A number of regulatory circuits in biological systems function through the exchange of phosphoryl groups from one protein to another. Spo0F and Spo0B are components of a phosphorelay that control sporulation in the bacterium Bacillus subtilis through the exchange of a phosphoryl group. Using beryllofluoride as a mimic for phosphorylation, we trapped the interaction of the phosphorylated Spo0F with Spo0B in the crystal lattice. The transition state of phosphoryl transfer continues to be a highly debated issue, as to whether it is associative or dissociative in nature. The geometry of Spo0F binding to Spo0B favors an associative mechanism for phosphoryl transfer. In order to visualize the autophosphorylation of the histidine kinase, KinA, and the subsequent phosphoryl transfer to Spo0F, we generated in silico models representing these reaction steps.


    Organizational Affiliation

    Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM-116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. kiv@scripps.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sporulation initiation phosphotransferase B
A, B, C, D
192Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: spo0B (spo0D)
EC: 2.7.-.-
Find proteins for P06535 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P06535
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sporulation initiation phosphotransferase F
E, F, G, H
124Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: spo0F
EC: 2.7.-.-
Find proteins for P06628 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P06628
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BFD
Query on BFD
E, F, G, H
L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.467α = 90.00
b = 118.331β = 90.00
c = 168.235γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Blu-Icedata collection
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-01-24 
  • Released Date: 2006-07-18 
  • Deposition Author(s): Varughese, K.I.

Revision History 

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance