2B5A | pdb_00002b5a

C.BclI, Control Element of the BclI Restriction-Modification System


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.201 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2B5A

This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of the Restriction-Modification System Control Element C.BclI and Mapping of Its Binding Site.

Sawaya, M.R.Zhu, Z.Mersha, F.Chan, S.H.Dabur, R.Xu, S.Y.Balendiran, G.K.

(2005) Structure 13: 1837-1847

  • DOI: https://doi.org/10.1016/j.str.2005.08.017
  • Primary Citation Related Structures: 
    2B5A

  • PubMed Abstract: 

    Protection from DNA invasion is afforded by restriction-modification systems in many bacteria. The efficiency of protection depends crucially on the relative expression levels of restriction versus methytransferase genes. This regulation is provided by a controller protein, named C protein. Studies of the Bcll system in E. coli suggest that C.Bcll functions as a negative regulator for M.Bcll expression, implying that it plays a role in defense against foreign DNA during virus infection. C.Bcll binds (Kd = 14.3 nM) to a 2-fold symmetric C box DNA sequence that overlaps with the putative -35 promoter region upstream of the bcllM and bcllC genes. The C.Bcll fold comprises five alpha helices: two helices form a helix-turn-helix motif, and the remaining three helices form the extensive dimer interface. The C.Bcll-DNA model proposed suggests that DNA bending might play an important role in gene regulation, and that Glu27 and Asp31 in C.Bcll might function critically in the regulation.


  • Organizational Affiliation
    • UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, 205 Boyer Hall, Box 951570, Los Angeles, California 90095, USA.

Macromolecule Content 

  • Total Structure Weight: 35.85 kDa 
  • Atom Count: 2,706 
  • Modeled Residue Count: 305 
  • Deposited Residue Count: 308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C.BclI
A, B, C, D
77[Bacillus] caldolyticusMutation(s): 0 
Gene Names: bclIC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.201 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.205α = 90
b = 65.016β = 90
c = 73.296γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations