4DUW

E. coli (lacZ) beta-galactosidase (G974A) in complex with allolactose

PDB DOI: https://doi.org/10.2210/pdb4DUW/pdb

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

Deposited: 2012-02-22 Released: 2013-03-20
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: 2.20 Å
R-Value Free: 0.213
R-Value Work: 0.160
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 487.03 kDa
Atom Count: 36,668
Modelled Residue Count: 4,060
Deposited Residue Count: 4,208
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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, lacA, lacZ EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12)) Explore P00722 Go to UniProtKB: P00722
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00722
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-6)-beta-D-glucopyranose	E, F, G, H	2		N/A	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G87251UV GlyCosmos: G87251UV GlyGen: G87251UV

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain AC [auth C] SDF format, chain AD [auth D] SDF format, chain BB [auth B] SDF format, chain BC [auth C] SDF format, chain BD [auth D] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain CC [auth C] SDF format, chain CD [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain DC [auth C] SDF format, chain DD [auth D] SDF format, chain EB [auth B] SDF format, chain EC [auth C] SDF format, chain ED [auth D] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain FC [auth C] SDF format, chain FD [auth D] SDF format, chain GB [auth B] SDF format, chain GC [auth C] SDF format, chain GD [auth D] SDF format, chain HB [auth B] SDF format, chain HC [auth C] SDF format, chain IC [auth C] SDF format, chain JB [auth B] SDF format, chain JC [auth C] SDF format, chain KB [auth B] SDF format, chain KC [auth C] SDF format, chain LB [auth B] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth C] SDF format, chain SC [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain TB [auth C] SDF format, chain TC [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth C] SDF format, chain UC [auth D] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth C] SDF format, chain VC [auth D] SDF format, chain W [auth A] SDF format, chain WB [auth C] SDF format, chain WC [auth D] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain XB [auth C] SDF format, chain XC [auth D] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain YB [auth C] SDF format, chain YC [auth D] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain ZC [auth D] SDF format, chain BA [auth A] SDF format, chain EA [auth A] SDF format, chain GA [auth A] SDF format, chain IB [auth B] SDF format, chain LC [auth C] SDF format, chain WA [auth B] SDF format, chain ZB [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth C] MOL2 format, chain AD [auth D] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth C] MOL2 format, chain BD [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth C] MOL2 format, chain CD [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth C] MOL2 format, chain DD [auth D] MOL2 format, chain EB [auth B] MOL2 format, chain EC [auth C] MOL2 format, chain ED [auth D] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth C] MOL2 format, chain FD [auth D] MOL2 format, chain GB [auth B] MOL2 format, chain GC [auth C] MOL2 format, chain GD [auth D] MOL2 format, chain HB [auth B] MOL2 format, chain HC [auth C] MOL2 format, chain IC [auth C] MOL2 format, chain JB [auth B] MOL2 format, chain JC [auth C] MOL2 format, chain KB [auth B] MOL2 format, chain KC [auth C] MOL2 format, chain LB [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain SC [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth C] MOL2 format, chain TC [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain UC [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain VC [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WB [auth C] MOL2 format, chain WC [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth C] MOL2 format, chain XC [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain YB [auth C] MOL2 format, chain YC [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain ZC [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain LC [auth C] MOL2 format, chain WA [auth B] MOL2 format, chain ZB [auth C]	AA [auth A] AB [auth B] AC [auth C] AD [auth D] BA [auth A] AA [auth A], AB [auth B], AC [auth C], AD [auth D], 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], FA [auth A], FB [auth B], FC [auth C], FD [auth D], GA [auth A], GB [auth B], GC [auth C], GD [auth D], HB [auth B], HC [auth C], IB [auth B], IC [auth C], JB [auth B], JC [auth C], KB [auth B], KC [auth C], LB [auth B], LC [auth C], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], SB [auth C], SC [auth D], T [auth A], TA [auth B], TB [auth C], TC [auth D], U [auth A], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], VC [auth D], W [auth A], WA [auth B], WB [auth C], WC [auth D], X [auth A], XA [auth B], XB [auth C], XC [auth D], Y [auth A], YA [auth B], YB [auth C], YC [auth D], Z [auth A], ZA [auth B], ZB [auth C], ZC [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AD [auth D] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain BC [auth C] Focus chain BD [auth D] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain CD [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain DD [auth D] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth C] Focus chain ED [auth D] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain FC [auth C] Focus chain FD [auth D] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain GC [auth C] Focus chain GD [auth D] Focus chain HB [auth B] Focus chain HC [auth C] Focus chain IB [auth B] Focus chain IC [auth C] Focus chain JB [auth B] Focus chain JC [auth C] Focus chain KB [auth B] Focus chain KC [auth C] Focus chain LB [auth B] Focus chain LC [auth C] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain VC [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain WC [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain XC [auth D] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain YC [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Focus chain ZC [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AD [auth D] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain BC [auth C] Focus chain BD [auth D] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain CD [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain DD [auth D] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth C] Focus chain ED [auth D] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain FC [auth C] Focus chain FD [auth D] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain GC [auth C] Focus chain GD [auth D] Focus chain HB [auth B] Focus chain HC [auth C] Focus chain IB [auth B] Focus chain IC [auth C] Focus chain JB [auth B] Focus chain JC [auth C] Focus chain KB [auth B] Focus chain KC [auth C] Focus chain LB [auth B] Focus chain LC [auth C] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain VC [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain WC [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain XC [auth D] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain YC [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Focus chain ZC [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain MB [auth C] SDF format, chain NB [auth C] SDF format, chain NC [auth D] SDF format, chain MC [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain MB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain NC [auth D] MOL2 format, chain MC [auth D]	HA [auth B] I [auth A] IA [auth B] J [auth A] JA [auth B] HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], MB [auth C], MC [auth D], NB [auth C], NC [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain NB [auth C] Focus chain NC [auth D] Interactions & Density Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain NB [auth C] Focus chain NC [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OB [auth C] SDF format, chain PB [auth C] SDF format, chain PC [auth D] SDF format, chain QB [auth C] SDF format, chain QC [auth D] SDF format, chain RB [auth C] SDF format, chain RC [auth D] SDF format, chain OC [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth C] MOL2 format, chain PB [auth C] MOL2 format, chain PC [auth D] MOL2 format, chain QB [auth C] MOL2 format, chain QC [auth D] MOL2 format, chain RB [auth C] MOL2 format, chain RC [auth D] MOL2 format, chain OC [auth D]	KA [auth B] L [auth A] LA [auth B] M [auth A] MA [auth B] KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OB [auth C], OC [auth D], PB [auth C], PC [auth D], QB [auth C], QC [auth D], RB [auth C], RC [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain RB [auth C] Focus chain RC [auth D] Interactions & Density Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain RB [auth C] Focus chain RC [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900041 Query on PRD_900041	E, F, G, H	beta-allolactose	Oligosaccharide / Inducer		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.213
R-Value Work: 0.160
R-Value Observed: 0.160
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.826	α = 90
b = 162.635	β = 90
c = 203.692	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-20
Type: Initial release
Version 1.1: 2013-07-10
Changes: Database references
Version 1.2: 2019-07-17
Changes: Data collection, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary