3I3D

E. COLI (lacZ) BETA-GALACTOSIDASE (M542A) IN COMPLEX WITH IPTG

• PDB DOI: https://doi.org/10.2210/pdb3I3D/pdb

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


• Deposited: 2009-06-30 Released: 2010-05-12 
• Deposition Author(s): Dugdale, M.L., Dymianiw, D., Minhas, B., Huber, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.232 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 479.56 kDa 
• Atom Count: 36,737 
• Modelled Residue Count: 4,044 
• Deposited Residue Count: 4,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	1,023	Escherichia coli K-12	Mutation(s): 1  Gene Names: lacz EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12)) Explore P00722  Go to UniProtKB:  P00722

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPT	E [auth A], F [auth A], SE [auth D], TE [auth D], UC [auth C], VA [auth B]	1-methylethyl 1-thio-beta-D-galactopyranoside C9 H18 O5 S BPHPUYQFMNQIOC-NXRLNHOXSA-N
DMS	AA [auth A], AC [auth B], AE [auth C], AG [auth D], BA [auth A], BC [auth B], BE [auth C], BF [auth D], BG [auth D], CA [auth A], CC [auth B], CD [auth C], CE [auth C], CF [auth D], CG [auth D], DA [auth A], DC [auth B], DD [auth C], DE [auth C], DF [auth D], DG [auth D], EA [auth A], EC [auth B], ED [auth C], EE [auth C], EF [auth D], EG [auth D], FA [auth A], FB [auth B], FC [auth B], FD [auth C], FE [auth C], FF [auth D], FG [auth D], GA [auth A], GB [auth B], GC [auth B], GD [auth C], GE [auth C], GF [auth D], GG [auth D], HA [auth A], HB [auth B], HC [auth B], HD [auth C], HE [auth C], HF [auth D], IA [auth A], IB [auth B], IC [auth B], ID [auth C], IE [auth C], IF [auth D], JA [auth A], JB [auth B], JC [auth B], JD [auth C], JE [auth C], JF [auth D], KA [auth A], KB [auth B], KC [auth B], KD [auth C], KE [auth C], KF [auth D], LA [auth A], LB [auth B], LC [auth B], LD [auth C], LE [auth C], LF [auth D], MA [auth A], MB [auth B], MC [auth B], MD [auth C], ME [auth C], MF [auth D], N [auth A], NA [auth A], NB [auth B], NC [auth B], ND [auth C], NE [auth C], NF [auth D], O [auth A], OA [auth A], OB [auth B], OC [auth B], OD [auth C], OE [auth C], OF [auth D], P [auth A], PA [auth A], PB [auth B], PC [auth B], PD [auth C], PE [auth C], PF [auth D], Q [auth A], QA [auth A], QB [auth B], QC [auth B], QD [auth C], QE [auth C], QF [auth D], R [auth A], RA [auth A], RB [auth B], RC [auth B], RD [auth C], RE [auth C], RF [auth D], S [auth A], SA [auth A], SB [auth B], SC [auth B], SD [auth C], SF [auth D], T [auth A], TA [auth A], TB [auth B], TC [auth B], TD [auth C], TF [auth D], U [auth A], UA [auth A], UB [auth B], UD [auth C], UF [auth D], V [auth A], VB [auth B], VD [auth C], VF [auth D], W [auth A], WB [auth B], WD [auth C], WF [auth D], X [auth A], XB [auth B], XD [auth C], XF [auth D], Y [auth A], YB [auth B], YD [auth C], YF [auth D], Z [auth A], ZB [auth B], ZD [auth C], ZF [auth D]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	G [auth A], H [auth A], I [auth A], UE [auth D], VC [auth C], VE [auth D], WA [auth B], WC [auth C], WE [auth D], XA [auth B], XC [auth C], YA [auth B], ZA [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	AB [auth B], AD [auth C], AF [auth D], BB [auth B], BD [auth C], CB [auth B], DB [auth B], EB [auth B], J [auth A], K [auth A], L [auth A], M [auth A], XE [auth D], YC [auth C], YE [auth D], ZC [auth C], ZE [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IPT	PDBBind:  3I3D	Ki: 1.03e+7 (nM) from 1 assay(s)
	BindingDB:  3I3D	Ki: 7.60e+4 (nM) from 1 assay(s)
	Binding MOAD:  3I3D	Ki: 1.03e+7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.232 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.54	α = 90
b = 162.39	β = 90
c = 203.73	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Dugdale, M.L., Dymianiw, D., Minhas, B., Huber, R.E.

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-10
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2021-10-13
  Changes: Database references, Structure summary
• Version 1.5: 2023-09-06
  Changes: Data collection, Refinement description