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 
  • R-Value Observed: 0.194 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/10.1007/s10930-009-9168-1
  • Primary Citation of Related Structures:  
    3CZJ

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, B, C, D
1,023Escherichia coli K-12Mutation(s): 1 
Gene Names: lacZb0344JW0335
EC: 3.2.1.23
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
149
Query on 149

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

Download Ideal Coordinates CCD File 
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]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
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]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

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