4DUV | pdb_00004duv

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 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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.

Macromolecule Content 

  • Total Structure Weight: 488.14 kDa 
  • Atom Count: 37,231 
  • Modeled Residue Count: 4,073 
  • Deposited Residue Count: 4,208 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, B, C, D
1,052Escherichia coli K-12Mutation(s): 1 
Gene Names: b0344, JW0335, lacZ
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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / 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
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
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
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
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
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

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Ligand Structure Quality Assessment 


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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
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-20
    Changes: Structure summary