1JYN

E. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH LACTOSE

PDB DOI: https://doi.org/10.2210/pdb1JYN/pdb

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

Deposited: 2001-09-13 Released: 2001-12-07
Deposition Author(s): Juers, D.H., Matthews, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.219
R-Value Work: 0.155

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 475.58 kDa
Atom Count: 37,546
Modelled Residue Count: 4,044
Deposited Residue Count: 4,092
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	1,023	Escherichia coli	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
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-(1-4)-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: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

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 AC [auth C] SDF format, chain AE [auth D] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain BE [auth D] SDF format, chain CA [auth A] SDF format, chain CC [auth C] SDF format, chain CE [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain DC [auth C] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain EC [auth C] 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 HA [auth A] SDF format, chain HB [auth B] SDF format, chain HC [auth C] SDF format, chain IA [auth A] SDF format, chain IB [auth B] SDF format, chain IC [auth C] SDF format, chain ID [auth D] SDF format, chain JA [auth A] SDF format, chain JB [auth B] SDF format, chain JC [auth C] SDF format, chain KA [auth A] SDF format, chain KB [auth B] SDF format, chain KC [auth C] SDF format, chain KD [auth D] SDF format, chain LA [auth A] SDF format, chain LB [auth B] SDF format, chain LC [auth C] SDF format, chain LD [auth D] SDF format, chain MA [auth A] SDF format, chain MB [auth B] SDF format, chain MC [auth C] SDF format, chain MD [auth D] SDF format, chain NB [auth B] SDF format, chain ND [auth D] SDF format, chain OB [auth B] SDF format, chain OC [auth C] SDF format, chain OD [auth D] SDF format, chain PB [auth B] SDF format, chain PC [auth C] SDF format, chain PD [auth D] SDF format, chain Q [auth A] SDF format, chain QB [auth B] SDF format, chain QC [auth C] SDF format, chain QD [auth D] SDF format, chain R [auth A] SDF format, chain RC [auth C] SDF format, chain RD [auth D] SDF format, chain S [auth A] SDF format, chain SC [auth C] SDF format, chain SD [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain TC [auth C] SDF format, chain TD [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UC [auth C] SDF format, chain UD [auth D] SDF format, chain V [auth A] SDF format, chain VC [auth C] SDF format, chain VD [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain WC [auth C] SDF format, chain WD [auth D] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain XC [auth C] SDF format, chain XD [auth D] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain YD [auth D] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain ZB [auth C] SDF format, chain AB [auth B] SDF format, chain BC [auth C] SDF format, chain CB [auth B] SDF format, chain GA [auth A] SDF format, chain HD [auth D] SDF format, chain JD [auth D] SDF format, chain NC [auth C] SDF format, chain VA [auth B] SDF format, chain ZD [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain AC [auth C] MOL2 format, chain AE [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain BE [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain CC [auth C] MOL2 format, chain CE [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain EC [auth C] 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 HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain HC [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain IC [auth C] MOL2 format, chain ID [auth D] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain JC [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain KC [auth C] MOL2 format, chain KD [auth D] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth B] MOL2 format, chain LC [auth C] MOL2 format, chain LD [auth D] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth B] MOL2 format, chain MC [auth C] MOL2 format, chain MD [auth D] MOL2 format, chain NB [auth B] MOL2 format, chain ND [auth D] MOL2 format, chain OB [auth B] MOL2 format, chain OC [auth C] MOL2 format, chain OD [auth D] MOL2 format, chain PB [auth B] MOL2 format, chain PC [auth C] MOL2 format, chain PD [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain QC [auth C] MOL2 format, chain QD [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RC [auth C] MOL2 format, chain RD [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SC [auth C] MOL2 format, chain SD [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TC [auth C] MOL2 format, chain TD [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UC [auth C] MOL2 format, chain UD [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VC [auth C] MOL2 format, chain VD [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain WC [auth C] MOL2 format, chain WD [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain XC [auth C] MOL2 format, chain XD [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain YD [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth C] MOL2 format, chain AB [auth B] MOL2 format, chain BC [auth C] MOL2 format, chain CB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain HD [auth D] MOL2 format, chain JD [auth D] MOL2 format, chain NC [auth C] MOL2 format, chain VA [auth B] MOL2 format, chain ZD [auth D]	AA [auth A] AB [auth B] AC [auth C] AE [auth D] BA [auth A] AA [auth A], AB [auth B], AC [auth C], AE [auth D], BA [auth A], BB [auth B], BC [auth C], BE [auth D], CA [auth A], CB [auth B], CC [auth C], CE [auth D], DA [auth A], DB [auth B], DC [auth C], EA [auth A], EB [auth B], EC [auth C], FA [auth A], FB [auth B], FC [auth C], FD [auth D], GA [auth A], GB [auth B], GC [auth C], GD [auth D], HA [auth A], HB [auth B], HC [auth C], HD [auth D], IA [auth A], IB [auth B], IC [auth C], ID [auth D], JA [auth A], JB [auth B], JC [auth C], JD [auth D], KA [auth A], KB [auth B], KC [auth C], KD [auth D], LA [auth A], LB [auth B], LC [auth C], LD [auth D], MA [auth A], MB [auth B], MC [auth C], MD [auth D], NB [auth B], NC [auth C], ND [auth D], OB [auth B], OC [auth C], OD [auth D], PB [auth B], PC [auth C], PD [auth D], Q [auth A], QB [auth B], QC [auth C], QD [auth D], R [auth A], RC [auth C], RD [auth D], S [auth A], SC [auth C], SD [auth D], T [auth A], TA [auth B], TC [auth C], TD [auth D], U [auth A], UA [auth B], UC [auth C], UD [auth D], V [auth A], VA [auth B], VC [auth C], VD [auth D], W [auth A], WA [auth B], WC [auth C], WD [auth D], X [auth A], XA [auth B], XC [auth C], XD [auth D], Y [auth A], YA [auth B], YD [auth D], Z [auth A], ZA [auth B], ZB [auth C], ZD [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 AE [auth D] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain BC [auth C] Focus chain BE [auth D] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain CE [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth C] 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 HA [auth A] Focus chain HB [auth B] Focus chain HC [auth C] Focus chain HD [auth D] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain IC [auth C] Focus chain ID [auth D] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain JC [auth C] Focus chain JD [auth D] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain KC [auth C] Focus chain KD [auth D] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain LC [auth C] Focus chain LD [auth D] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain MC [auth C] Focus chain MD [auth D] Focus chain NB [auth B] Focus chain NC [auth C] Focus chain ND [auth D] Focus chain OB [auth B] Focus chain OC [auth C] Focus chain OD [auth D] Focus chain PB [auth B] Focus chain PC [auth C] Focus chain PD [auth D] Focus chain Q [auth A] Focus chain QB [auth B] Focus chain QC [auth C] Focus chain QD [auth D] Focus chain R [auth A] Focus chain RC [auth C] Focus chain RD [auth D] Focus chain S [auth A] Focus chain SC [auth C] Focus chain SD [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TC [auth C] Focus chain TD [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UC [auth C] Focus chain UD [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VC [auth C] Focus chain VD [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WC [auth C] Focus chain WD [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XC [auth C] Focus chain XD [auth D] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YD [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Focus chain ZD [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AE [auth D] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain BC [auth C] Focus chain BE [auth D] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain CE [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth C] 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 HA [auth A] Focus chain HB [auth B] Focus chain HC [auth C] Focus chain HD [auth D] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain IC [auth C] Focus chain ID [auth D] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain JC [auth C] Focus chain JD [auth D] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain KC [auth C] Focus chain KD [auth D] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain LC [auth C] Focus chain LD [auth D] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain MC [auth C] Focus chain MD [auth D] Focus chain NB [auth B] Focus chain NC [auth C] Focus chain ND [auth D] Focus chain OB [auth B] Focus chain OC [auth C] Focus chain OD [auth D] Focus chain PB [auth B] Focus chain PC [auth C] Focus chain PD [auth D] Focus chain Q [auth A] Focus chain QB [auth B] Focus chain QC [auth C] Focus chain QD [auth D] Focus chain R [auth A] Focus chain RC [auth C] Focus chain RD [auth D] Focus chain S [auth A] Focus chain SC [auth C] Focus chain SD [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TC [auth C] Focus chain TD [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UC [auth C] Focus chain UD [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VC [auth C] Focus chain VD [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WC [auth C] Focus chain WD [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XC [auth C] Focus chain XD [auth D] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YD [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Focus chain ZD [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BD [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain OA [auth B] SDF format, chain RB [auth C] SDF format, chain SB [auth C] SDF format, chain TB [auth C] SDF format, chain UB [auth C] SDF format, chain ZC [auth D] SDF format, chain AD [auth D] SDF format, chain NA [auth B] SDF format, chain P [auth A] SDF format, chain YC [auth D] MOL2 format, chain BD [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain SB [auth C] MOL2 format, chain TB [auth C] MOL2 format, chain UB [auth C] MOL2 format, chain ZC [auth D] MOL2 format, chain AD [auth D] MOL2 format, chain NA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain YC [auth D]	AD [auth D] BD [auth D] I [auth A] J [auth A] K [auth A] AD [auth D], BD [auth D], I [auth A], J [auth A], K [auth A], NA [auth B], OA [auth B], P [auth A], RB [auth C], SB [auth C], TB [auth C], UB [auth C], YC [auth D], ZC [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AD [auth D] Focus chain BD [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain RB [auth C] Focus chain SB [auth C] Focus chain TB [auth C] Focus chain UB [auth C] Focus chain YC [auth D] Focus chain ZC [auth D] Interactions & Density Focus chain AD [auth D] Focus chain BD [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain RB [auth C] Focus chain SB [auth C] Focus chain TB [auth C] Focus chain UB [auth C] Focus chain YC [auth D] Focus chain ZC [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain CD [auth D] SDF format, chain DD [auth D] SDF format, chain ED [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain VB [auth C] SDF format, chain WB [auth C] SDF format, chain XB [auth C] SDF format, chain YB [auth C] MOL2 format, chain CD [auth D] MOL2 format, chain DD [auth D] MOL2 format, chain ED [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain WB [auth C] MOL2 format, chain XB [auth C] MOL2 format, chain YB [auth C]	CD [auth D] DD [auth D] ED [auth D] L [auth A] M [auth A] CD [auth D], DD [auth D], ED [auth D], L [auth A], M [auth A], N [auth A], O [auth A], PA [auth B], QA [auth B], RA [auth B], SA [auth B], VB [auth C], WB [auth C], XB [auth C], YB [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CD [auth D] Focus chain DD [auth D] Focus chain ED [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain VB [auth C] Focus chain WB [auth C] Focus chain XB [auth C] Focus chain YB [auth C] Interactions & Density Focus chain CD [auth D] Focus chain DD [auth D] Focus chain ED [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain VB [auth C] Focus chain WB [auth C] Focus chain XB [auth C] Focus chain YB [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004 Query on PRD_900004	E, F, G, H	beta-lactose	Oligosaccharide / Nutrient		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: 1.80 Å
R-Value Free: 0.219
R-Value Work: 0.155
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.55	α = 90
b = 168.63	β = 90
c = 200.88	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement
MOSFLM	data reduction
CCP4	data scaling
TNT	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2001-12-07

Deposition Author(s):

Juers, D.H.

Matthews, B.W.

Revision History (Full details and data files)

Version 1.0: 2001-12-07
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2021-10-27
Changes: Database references, Structure summary
Version 2.2: 2024-02-07
Changes: Data collection