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- PDB-7uz1: Structure of beta-glycosidase from Sulfolobus solfataricus in com... -

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Basic information

Entry
Database: PDB / ID: 7uz1
TitleStructure of beta-glycosidase from Sulfolobus solfataricus in complex with C5a-bromo-valienide.
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Covalent Inhibition / Glycoside Hydrolase
Function / homology
Function and homology information


beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
: / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-OM0 / Beta-galactosidase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsDanby, P.M. / Jeong, A. / Sim, L. / Sweeney, R.P. / Wardman, J.F. / Karimi, R. / Geissner, A. / Worrall, L.J. / Strynadka, N.C.J. / Withers, S.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Vinyl Halide-Modified Unsaturated Cyclitols are Mechanism-Based Glycosidase Inhibitors.
Authors: Danby, P.M. / Jeong, A. / Sim, L. / Sweeney, R.P. / Wardman, J.F. / Karimi, R. / Geissner, A. / Worrall, L.J. / Reid, J.P. / Strynadka, N.C.J. / Withers, S.G.
History
DepositionMay 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2255
Polymers113,6532
Non-polymers5723
Water7,062392
1
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0822
Polymers56,8261
Non-polymers2551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1443
Polymers56,8261
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.088, 168.088, 95.548
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Beta-galactosidase / Glycoside hydrolase family 1 protein


Mass: 56826.465 Da / Num. of mol.: 2 / Mutation: A235H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea)
Gene: HFC64_10340, SSOP1_3114, SULA_0798, SULB_0800, SULC_0798, SULZ_04135
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3K5E4
#2: Chemical ChemComp-OM0 / (1R,2S,3R,4R)-5-bromo-6-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol / C5a-bromo-valienide


Mass: 255.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11BrO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 10 - 13 % PEG 4000, 0.1 M Sodium Acetate, 0.2M Ammonium Acetate, 5% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.58→46.4 Å / Num. obs: 211061 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 1 / Rmerge(I) obs: 0.025 / Net I/σ(I): 12.2
Reflection shellResolution: 1.58→1.62 Å / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 10372 / CC1/2: 0.37 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UWR

1uwr


Resolution: 1.58→43.301 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.204 / SU B: 1.941 / SU ML: 0.064 / Average fsc free: 0.8704 / Average fsc work: 0.8769 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2123 10231 4.848 %
Rwork0.1894 200792 -
all0.19 --
obs-211023 99.868 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.763 Å2
Baniso -1Baniso -2Baniso -3
1--0.345 Å2-0.173 Å2-0 Å2
2---0.345 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.58→43.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7941 0 28 392 8361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138230
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157294
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.64311197
X-RAY DIFFRACTIONr_angle_other_deg1.5021.5816727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9565976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17321.247489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.512151238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7751562
X-RAY DIFFRACTIONr_chiral_restr0.0970.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022141
X-RAY DIFFRACTIONr_nbd_refined0.2090.21551
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.26814
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23943
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23708
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2333
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.210
X-RAY DIFFRACTIONr_nbd_other0.2290.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.211
X-RAY DIFFRACTIONr_mcbond_it3.0313.4153910
X-RAY DIFFRACTIONr_mcbond_other3.0283.4143909
X-RAY DIFFRACTIONr_mcangle_it3.6995.1174884
X-RAY DIFFRACTIONr_mcangle_other3.7015.1184885
X-RAY DIFFRACTIONr_scbond_it4.0723.7074320
X-RAY DIFFRACTIONr_scbond_other4.0723.7074321
X-RAY DIFFRACTIONr_scangle_it5.7125.4216313
X-RAY DIFFRACTIONr_scangle_other5.7115.4216314
X-RAY DIFFRACTIONr_lrange_it6.5538.6159377
X-RAY DIFFRACTIONr_lrange_other6.54838.4799323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.6210.3417770.34414804X-RAY DIFFRACTION99.9936
1.621-1.6650.3047150.31114425X-RAY DIFFRACTION99.9934
1.665-1.7140.2997010.29114003X-RAY DIFFRACTION100
1.714-1.7660.2867120.2713617X-RAY DIFFRACTION100
1.766-1.8240.2816420.25213233X-RAY DIFFRACTION99.9928
1.824-1.8880.2676540.24212742X-RAY DIFFRACTION99.8137
1.888-1.960.2766510.22712317X-RAY DIFFRACTION100
1.96-2.040.2616090.22111858X-RAY DIFFRACTION100
2.04-2.130.2585960.2211393X-RAY DIFFRACTION100
2.13-2.2340.2235430.20410921X-RAY DIFFRACTION100
2.234-2.3550.2415430.20310393X-RAY DIFFRACTION100
2.355-2.4980.2235190.1889798X-RAY DIFFRACTION99.9419
2.498-2.670.2255010.1859198X-RAY DIFFRACTION99.8045
2.67-2.8840.2034060.1768655X-RAY DIFFRACTION100
2.884-3.1590.2213880.1857969X-RAY DIFFRACTION100
3.159-3.5320.2143460.1917228X-RAY DIFFRACTION100
3.532-4.0780.1593070.1636374X-RAY DIFFRACTION100
4.078-4.9940.1442870.1335395X-RAY DIFFRACTION99.2489
4.994-7.0580.1892350.1664192X-RAY DIFFRACTION99.7297
7.058-43.3010.282990.222277X-RAY DIFFRACTION93.2862

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