2O3O | pdb_00002o3o

Crystal Structure of the sensor histidine kinase regulator YycI from Bacillus subtitlis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 
    0.262 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

The Crystal Structure of Bacillus subtilis YycI Reveals a Common Fold for Two Members of an Unusual Class of Sensor Histidine Kinase Regulatory Proteins.

Santelli, E., Liddington, R.C., Mohan, M.A., Hoch, J.A., Szurmant, H.

(2007) J Bacteriol 189: 3290-3295

  • DOI: https://doi.org/10.1128/JB.01937-06
  • Primary Citation Related Structures: 
    2O3O

  • PubMed Abstract: 

    YycI and YycH are two membrane-anchored periplasmic proteins that regulate the essential Bacillus subtilis YycG histidine kinase through direct interaction. Here we present the crystal structure of YycI at a 2.9-A resolution. YycI forms a dimer, and remarkably the structure resembles that of the two C-terminal domains of YycH despite nearly undetectable sequence homology (10%) between the two proteins.

    • Organizational Affiliation: 
    • Division of Cellular Biology, Mail code MEM-116, Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 355.85 kDa 
  • Atom Count: 23,401 
  • Modeled Residue Count: 2,871 
  • Deposited Residue Count: 3,048 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
YycI protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
254Bacillus subtilisMutation(s): 6 
Gene Names: yycI
UniProt
Find proteins for Q45612 (Bacillus subtilis (strain 168))
Explore Q45612 
Go to UniProtKB:  Q45612
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45612
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.262 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.792α = 90
b = 161.922β = 90.9
c = 180.156γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary