3CZJ

E. COLI (lacZ) BETA-GALACTOSIDASE (N460T) IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-beta-Galactosidase (E. coli) as Examples.

Kappelhoff, J.C.Liu, S.Y.Dugdale, M.L.Dymianiw, D.L.Linton, L.R.Huber, R.E.

(2009) Protein J. 28: 96-103

  • DOI: 10.1007/s10930-009-9168-1

  • PubMed Abstract: 
  • The values of the rate constants and the associated enthalpies and entropies of enzymes with two catalytic steps can be measured by determining the effects of temperature on the k (cat) values. Practical considerations that should be taken into accou ...

    The values of the rate constants and the associated enthalpies and entropies of enzymes with two catalytic steps can be measured by determining the effects of temperature on the k (cat) values. Practical considerations that should be taken into account when doing this are presented. The narrow temperature range available with enzymes and the sensitivity of pH to temperature mean that special attention to detail must be taken and this study highlights the assiduousness needed. The necessity of conversion of apparent k (cat) to true k (cat) values when assays are done with products having pKa values near to the assay pH is shown and the importance of obtaining sufficient data is emphasized. Reasons that non-linear regression should be used to obtain the estimates of rate constants and activation thermodynamic parameters are given. Other precautions and recommendations are also presented. Results obtained by this method for native beta-galactosidase (E. coli) and for a beta-galactosidase in which a Thr was substituted for Asn-460 were analyzed to demonstrate the valuable mechanistic details of enzymes that can be obtained from studies of this type.


    Organizational Affiliation

    Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase
A, B, C, D
1023Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: lacZ
EC: 3.2.1.23
Find proteins for P00722 (Escherichia coli (strain K12))
Go to UniProtKB:  P00722
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
149
Query on 149

Download SDF File 
Download CCD File 
A, B, C, D
D-galactonolactone
(3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-one
C6 H10 O6
PHOQVHQSTUBQQK-MGCNEYSASA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B, C, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 151.443α = 90.00
b = 161.643β = 90.00
c = 202.155γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
ADSCdata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2018-01-24
    Type: Structure summary
  • Version 1.3: 2018-09-05
    Type: Data collection, Structure summary