4DUV

E. coli (lacZ) beta-galactosidase (G974A) 2-deoxy-galactosyl-enzyme and bis-Tris complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The Glucose Acceptor site of lacZ beta-galactosidase for the synthesis of allolactose - the natural inducer of the lac operon

Wheatley, R.W.Lo, S.Janzcewicz, L.J.Dugdale, M.L.Huber, R.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-galactosidaseA, B, C, D1,052Escherichia coli K-12Mutation(s): 1 
Gene Names: b0344JW0335lacZ
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB

Download Ideal Coordinates CCD File 
F [auth A],
GA [auth B],
NB [auth C],
UC [auth D]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
2DG
Query on 2DG

Download Ideal Coordinates CCD File 
E [auth A],
FA [auth B],
MB [auth C],
TC [auth D]
2-deoxy-alpha-D-galactopyranose
C6 H12 O5
PMMURAAUARKVCB-ARQDHWQXSA-N
 Ligand Interaction
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],
BD [auth D],
CA [auth A],
CB [auth B],
CC [auth C],
CD [auth D],
DA [auth A],
DB [auth B],
DC [auth C],
DD [auth D],
EA [auth A],
EB [auth B],
EC [auth C],
ED [auth D],
FB [auth B],
FC [auth C],
FD [auth D],
GB [auth B],
GC [auth C],
GD [auth D],
HB [auth B],
HC [auth C],
HD [auth D],
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],
LB [auth B],
LC [auth C],
LD [auth D],
M [auth A],
MC [auth C],
MD [auth D],
N [auth A],
NC [auth C],
ND [auth D],
O [auth A],
OA [auth B],
OC [auth C],
OD [auth D],
P [auth A],
PA [auth B],
PC [auth C],
PD [auth D],
Q [auth A],
QA [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],
TD [auth D],
U [auth A],
UA [auth B],
UB [auth C],
UD [auth D],
V [auth A],
VA [auth B],
VB [auth C],
VD [auth D],
W [auth A],
WA [auth B],
WB [auth C],
WD [auth D],
X [auth A],
XA [auth B],
XB [auth C],
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
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
HA [auth B],
IA [auth B],
JA [auth B],
G [auth A],
H [auth A],
HA [auth B],
IA [auth B],
JA [auth B],
OB [auth C],
PB [auth C],
VC [auth D],
WC [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AD [auth D],
I [auth A],
J [auth A],
K [auth A],
KA [auth B],
AD [auth D],
I [auth A],
J [auth A],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
MA [auth B],
NA [auth B],
QB [auth C],
RB [auth C],
SB [auth C],
TB [auth C],
XC [auth D],
YC [auth D],
ZC [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.57α = 90
b = 167.731β = 90
c = 201.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations, Structure summary