1HN1

E. COLI (LAC Z) BETA-GALACTOSIDASE (ORTHORHOMBIC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions.

Juers, D.H.Matthews, B.W.

(2001) J Mol Biol 311: 851-862

  • DOI: 10.1006/jmbi.2001.4891
  • Primary Citation of Related Structures:  
    1HN1

  • PubMed Abstract: 
  • Flash-freezing, which has become routine in macromolecular X-ray crystallography, causes the crystal to contract substantially. In the case of Escherichia coli beta-galactosidase the changes are reversible and are shown to be due to lattice repacking ...

    Flash-freezing, which has become routine in macromolecular X-ray crystallography, causes the crystal to contract substantially. In the case of Escherichia coli beta-galactosidase the changes are reversible and are shown to be due to lattice repacking. On cooling, the area of the protein surface involved in lattice contacts increases by 50 %. There are substantial alterations in intermolecular contacts, these changes being dominated by the long, polar side-chains. For entropic reasons such side-chains, as well as surface solvent molecules, tend to be somewhat disordered at room temperature but can form extensive hydrogen-bonded networks on cooling. Low-temperature density measurements suggest that, at least in some cases, the beneficial effect of cryosolvents may be due to a density increase on vitrification which reduces the volume of bulk solvent that needs to be expelled from the crystal. Analysis of beta-galactosidase and several other proteins suggests that both intramolecular and intermolecular contact interfaces can be perturbed by cryocooling but that the changes tend to be more dramatic in the latter case. The temperature-dependence of the intermolecular interactions suggests that caution may be necessary in interpreting protein-protein and protein-nucleic acid interactions based on low-temperature crystal structures.


    Related Citations: 
    • High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation
      JUERS, D.H., JACOBSON, R.H., WIGLEY, D., ZHANG, X.J., HUBER, R.E., TRONRUD, D.E., MATTHEWS, B.W.
      (2000) Protein Sci 9: 1685
    • Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases
      JUERS, D.H., HUBER, R.E., MATTHEWS, B.W.
      (1999) Protein Sci 8: 122
    • Three-dimensional structure of beta-galactosidase from E. coli.
      JACOBSON, R.H., ZHANG, X.J., DUBOSE, R.F., MATTHEWS, B.W.
      (1994) Nature 369: 761
    • Crystallization of beta-galactosidase from Escherichia coli.
      JACOBSON, R.H., MATTHEWS, B.W.
      (1992) J Mol Biol 223: 1177

    Organizational Affiliation

    Institute of Molecular Biology Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene, OR 97403-1229, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-GALACTOSIDASEABCD1023Escherichia coliMutation(s): 0 
Gene Names: LAC Z
EC: 3.1.2.23 (PDB Primary Data), 3.2.1.23 (UniProt)
Find proteins for P00722 (Escherichia coli (strain K12))
Explore P00722 
Go to UniProtKB:  P00722
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.9α = 90
b = 171.4β = 90
c = 204.5γ = 90
Software Package:
Software NamePurpose
TNTrefinement
SCALEPACKdata scaling
TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2017-11-29
    Changes: Database references