8RI7

Beta-galactosidase (LacZ) in complex with galactosyrin from Pseudomonas syringae.

PDB DOI: https://doi.org/10.2210/pdb8RI7/pdb
EM Map EMD-19182: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-18 Released: 2025-01-01
Deposition Author(s): Hardenbrook, N.J., Sheng, Y., Zhang, P.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.93 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Identification of a novel inhibitor for beta-galactosidase from Pseudomonas syringae.

Hardenbrook, N.J., Sheng, Y., Sanguankiattichai, N., Zhang, P., Preston, G., van der Hoorn, R.

To be published.

Macromolecule Content

Total Structure Weight: 470.56 kDa
Atom Count: 33,710
Modelled Residue Count: 4,064
Deposited Residue Count: 4,120
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	1,030	Escherichia coli	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00722
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H05 (Subject of Investigation/LOI) Query on A1H05 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D]	E [auth A], J [auth B], O [auth C], T [auth D]	(2S,3R,4S)-2-[bis(oxidanyl)methyl]pyrrolidine-3,4-diol C₅ H₁₁ N O₄ GRHIWHJZSCBMFQ-HZLVTQRSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	F [auth A] G [auth A] K [auth B] L [auth B] P [auth C] F [auth A], G [auth A], K [auth B], L [auth B], P [auth C], Q [auth C], U [auth D], V [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	H [auth A] I [auth A] M [auth B] N [auth B] R [auth C] H [auth A], I [auth A], M [auth B], N [auth B], R [auth C], S [auth C], W [auth D], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 1.93 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-01

Deposition Author(s):

Hardenbrook, N.J.

Sheng, Y.

Zhang, P.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T015128/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R017913/1
European Research Council (ERC)	European Union	101021133
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54 AI170791-7522
Wellcome Trust	United Kingdom	206422/Z/17/Z