Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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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: https://doi.org/10.1007/s10930-009-9168-1
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
1,023Escherichia coli K-12Mutation(s): 1 
Gene Names: lacZb0344JW0335
Find proteins for P00722 (Escherichia coli (strain K12))
Explore P00722 
Go to UniProtKB:  P00722
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00722
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 149

Download Ideal Coordinates CCD File 
E [auth A],
JA [auth B],
RB [auth C],
XC [auth D]
C6 H10 O6
Query on DMS

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AA [auth A]
AB [auth B]
AC [auth C]
BA [auth A]
BB [auth B]
AA [auth A],
AB [auth B],
AC [auth C],
BA [auth A],
BB [auth B],
BC [auth C],
CA [auth A],
CB [auth B],
CC [auth C],
DA [auth A],
DB [auth B],
DC [auth C],
EA [auth A],
EB [auth B],
EC [auth C],
ED [auth D],
FA [auth A],
FB [auth B],
FC [auth C],
FD [auth D],
GA [auth A],
GB [auth B],
GC [auth C],
GD [auth D],
HA [auth A],
HB [auth B],
HC [auth C],
HD [auth D],
IA [auth A],
IB [auth B],
IC [auth C],
ID [auth D],
JB [auth B],
JC [auth C],
JD [auth D],
KB [auth B],
KC [auth C],
KD [auth D],
L [auth A],
LB [auth B],
LC [auth C],
LD [auth D],
M [auth A],
MB [auth B],
MC [auth C],
MD [auth D],
N [auth A],
NB [auth B],
NC [auth C],
ND [auth D],
O [auth A],
OB [auth B],
OC [auth C],
OD [auth D],
P [auth A],
PB [auth B],
PC [auth C],
PD [auth D],
Q [auth A],
QB [auth B],
QC [auth C],
QD [auth D],
R [auth A],
RA [auth B],
RC [auth C],
RD [auth D],
S [auth A],
SA [auth B],
SC [auth C],
SD [auth D],
T [auth A],
TA [auth B],
TC [auth C],
TD [auth D],
U [auth A],
UA [auth B],
UC [auth C],
UD [auth D],
V [auth A],
VA [auth B],
VC [auth C],
VD [auth D],
W [auth A],
WA [auth B],
WC [auth C],
WD [auth D],
X [auth A],
XA [auth B],
Y [auth A],
YA [auth B],
YB [auth C],
Z [auth A],
ZA [auth B],
ZB [auth C]
C2 H6 O S
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
KA [auth B]
LA [auth B]
MA [auth B]
F [auth A],
G [auth A],
KA [auth B],
LA [auth B],
MA [auth B],
SB [auth C],
TB [auth C],
YC [auth D],
ZC [auth D]
Query on NA

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AD [auth D]
BD [auth D]
CD [auth D]
DD [auth D]
H [auth A]
AD [auth D],
BD [auth D],
CD [auth D],
DD [auth D],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
NA [auth B],
OA [auth B],
PA [auth B],
QA [auth B],
UB [auth C],
VB [auth C],
WB [auth C],
XB [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.443α = 90
b = 161.643β = 90
c = 202.155γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2018-09-05
    Changes: Data collection, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations
  • Version 1.5: 2021-10-20
    Changes: Database references
  • Version 1.6: 2023-08-30
    Changes: Data collection, Refinement description