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- PDB-8ri7: Beta-galactosidase (LacZ) in complex with glycosyrin from Pseudom... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8ri7
TitleBeta-galactosidase (LacZ) in complex with glycosyrin from Pseudomonas syringae.
ComponentsBeta-galactosidase
KeywordsHYDROLASE / beta-galactosidase / inhibitor / iminosugar / plant pathogenic bacteria.
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site ...Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.93 Å
AuthorsHardenbrook, N.J. / Sheng, Y. / Zhang, P.
Funding support United Kingdom, European Union, United States, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T015128/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R017913/1 United Kingdom
European Research Council (ERC)101021133European Union
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170791-7522 United States
Wellcome Trust206422/Z/17/Z United Kingdom
CitationJournal: To Be Published
Title: Identification of a novel inhibitor for beta-galactosidase from Pseudomonas syringae.
Authors: Hardenbrook, N.J. / Sheng, Y. / Sanguankiattichai, N. / Zhang, P. / Preston, G. / van der Hoorn, R.
History
DepositionDec 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / em_admin ...chem_comp / em_admin / pdbx_database_related / pdbx_struct_conn_angle / struct / struct_conn
Item: _chem_comp.pdbx_synonyms / _em_admin.last_update ..._chem_comp.pdbx_synonyms / _em_admin.last_update / _em_admin.title / _pdbx_database_related.details / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,56424
Polymers469,5894
Non-polymers97520
Water18,3391018
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Beta-galactosidase / Beta-gal / Lactase


Mass: 117397.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lacZ, b0344, JW0335 / Production host: Escherichia coli (E. coli) / References: UniProt: P00722, beta-galactosidase
#2: Chemical
ChemComp-A1H05 / (2S,3R,4S)-2-[bis(oxidanyl)methyl]pyrrolidine-3,4-diol / glycosyrin hydrate form


Mass: 149.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1018 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: beta-galactosidase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Details: 25 mM Tris, 50 mM NaCl, 2 mM MgCl2, 2 mM EDTA, 1 mM TCEP, pH 8.0
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7Coot0.9.6model fitting
9PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 659661 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Initial model built using ModelAngelo / Source name: Other / Type: other
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00633628
ELECTRON MICROSCOPYf_angle_d0.7945876
ELECTRON MICROSCOPYf_dihedral_angle_d13.78912124
ELECTRON MICROSCOPYf_chiral_restr0.0494812
ELECTRON MICROSCOPYf_plane_restr0.0086044

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