4DUV | pdb_00004duv

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

• PDB DOI: https://doi.org/10.2210/pdb4DUV/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-02-22 Released: 2013-04-03 
• Deposition Author(s): Wheatley, R.W., Lo, S., Janzcewicz, L.J., Dugdale, M.L., Huber, R.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	1,052	Escherichia coli K-12	Mutation(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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	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	E [auth A], FA [auth B], MB [auth C], TC [auth D]	2-deoxy-alpha-D-galactopyranose C6 H12 O5 PMMURAAUARKVCB-ARQDHWQXSA-N
DMS	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	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	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), 0.210 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.57	α = 90
b = 167.731	β = 90
c = 201.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Wheatley, R.W., Lo, S., Janzcewicz, L.J., Dugdale, M.L., Huber, R.E.

Revision History  

• 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