3DYO

E. coli (lacZ) beta-galactosidase (H418N) in complex with IPTG

• PDB DOI: https://doi.org/10.2210/pdb3DYO/pdb

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


• Deposited: 2008-07-28 Released: 2008-10-28 
• Deposition Author(s): Juers, D.H., Huber, R.E., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.173 

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: 477.12 kDa 
• Atom Count: 36,820 
• 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, b0344, JW0335 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	HC [auth C], HD [auth C], IC [auth C], M [auth A], MA [auth A], N [auth A], PD [auth D], QD [auth D], RD [auth D], WA [auth B], XA [auth B], YB [auth B]	1-methylethyl 1-thio-beta-D-galactopyranoside C9 H18 O5 S BPHPUYQFMNQIOC-NXRLNHOXSA-N
DMS	AA [auth A], AB [auth B], AD [auth C], AE [auth D], BA [auth A], BB [auth B], BD [auth C], BE [auth D], CA [auth A], CB [auth B], CD [auth C], CE [auth D], DA [auth A], DB [auth B], DD [auth C], DE [auth D], EA [auth A], EB [auth B], ED [auth C], EE [auth D], FA [auth A], FB [auth B], FD [auth C], FE [auth D], GA [auth A], GB [auth B], GD [auth C], GE [auth D], HA [auth A], HB [auth B], HE [auth D], IA [auth A], IB [auth B], IE [auth D], JA [auth A], JB [auth B], JC [auth C], JE [auth D], KA [auth A], KB [auth B], KC [auth C], KE [auth D], LA [auth A], LB [auth B], LC [auth C], LE [auth D], MB [auth B], MC [auth C], ME [auth D], NB [auth B], NC [auth C], NE [auth D], O [auth A], OB [auth B], OC [auth C], OE [auth D], P [auth A], PB [auth B], PC [auth C], Q [auth A], QB [auth B], QC [auth C], R [auth A], RB [auth B], RC [auth C], S [auth A], SB [auth B], SC [auth C], SD [auth D], T [auth A], TB [auth B], TC [auth C], TD [auth D], U [auth A], UB [auth B], UC [auth C], UD [auth D], V [auth A], VB [auth B], VC [auth C], VD [auth D], W [auth A], WB [auth B], WC [auth C], WD [auth D], X [auth A], XB [auth B], XC [auth C], XD [auth D], Y [auth A], YA [auth B], YC [auth C], YD [auth D], Z [auth A], ZA [auth B], ZC [auth C], ZD [auth D]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	AC [auth C], BC [auth C], E [auth A], F [auth A], G [auth A], H [auth A], ID [auth D], JD [auth D], KD [auth D], NA [auth B], OA [auth B], PA [auth B], QA [auth B], ZB [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	CC [auth C], DC [auth C], EC [auth C], FC [auth C], GC [auth C], I [auth A], J [auth A], K [auth A], L [auth A], LD [auth D], MD [auth D], ND [auth D], OD [auth D], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IPT	BindingDB:  3DYO	Ki: 7.60e+4 (nM) from 1 assay(s)
	Binding MOAD:  3DYO	Ki: 5.00e+6 (nM) from 1 assay(s)
	PDBBind:  3DYO	Ki: 5.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.01	α = 90
b = 162.52	β = 90
c = 204.01	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement
MOSFLM	data reduction
SCALA	data scaling
TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Juers, D.H., Huber, R.E., Matthews, B.W.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2021-07-28
  Changes: Refinement description, Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description