1VZY | pdb_00001vzy

Crystal structure of the Bacillus subtilis HSP33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.225 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.210 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1VZY

This is version 1.3 of the entry. See complete history

Literature

The crystal structure of the reduced, Zn2+-bound form of the B. subtilis Hsp33 chaperone and its implications for the activation mechanism.

Janda, I.Devedjiev, Y.Derewenda, U.Dauter, Z.Bielnicki, J.Cooper, D.R.Graf, P.C.Joachimiak, A.Jakob, U.Derewenda, Z.S.

(2004) Structure 12: 1901-1907

  • DOI: https://doi.org/10.1016/j.str.2004.08.003
  • Primary Citation Related Structures: 
    1VZY

  • PubMed Abstract: 

    The bacterial heat shock protein Hsp33 is a redox-regulated chaperone activated by oxidative stress. In response to oxidation, four cysteines within a Zn2+ binding C-terminal domain form two disulfide bonds with concomitant release of the metal. This leads to the formation of the biologically active Hsp33 dimer. The crystal structure of the N-terminal domain of the E. coli protein has been reported, but neither the structure of the Zn2+ binding motif nor the nature of its regulatory interaction with the rest of the protein are known. Here we report the crystal structure of the full-length B. subtilis Hsp33 in the reduced form. The structure of the N-terminal, dimerization domain is similar to that of the E. coli protein, although there is no domain swapping. The Zn2+ binding domain is clearly resolved showing the details of the tetrahedral coordination of Zn2+ by four thiolates. We propose a structure-based activation pathway for Hsp33.


  • Organizational Affiliation
    • Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Macromolecule Content 

  • Total Structure Weight: 63.95 kDa 
  • Atom Count: 4,685 
  • Modeled Residue Count: 576 
  • Deposited Residue Count: 582 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
33 KDA CHAPERONIN
A, B
291Bacillus subtilis subsp. subtilis str. 168Mutation(s): 2 
UniProt
Find proteins for P37565 (Bacillus subtilis (strain 168))
Explore P37565 
Go to UniProtKB:  P37565
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37565
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.225 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.292α = 90
b = 115.292β = 90
c = 106.441γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-06
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations