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- PDB-7uz2: Structure of beta-glycosidase from Sulfolobus solfataricus in com... -

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Basic information

Entry
Database: PDB / ID: 7uz2
TitleStructure of beta-glycosidase from Sulfolobus solfataricus in complex with C5a-fluoro-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-OML / Beta-galactosidase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsDanby, P.M. / Jeong, A. / Sim, L. / Sweeney, R.P. / Wardman, J.F. / 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 16, 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)114,0414
Polymers113,6532
Non-polymers3882
Water6,125340
1
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0212
Polymers56,8261
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0212
Polymers56,8261
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.265, 168.265, 95.504
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-OML / (1R,2S,3R,4R)-5-fluoro-6-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol / C5a-fluoro-valienide


Mass: 194.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11FO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 293 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: 1.83→47.8 Å / Num. obs: 136568 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.027 / Net I/σ(I): 11.6
Reflection shellResolution: 1.83→1.88 Å / Rmerge(I) obs: 1.115 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 6735 / CC1/2: 0.28 / % possible all: 99.9

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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: 1.83→45.419 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.211 / SU B: 4.186 / SU ML: 0.115 / Average fsc free: 0.8168 / Average fsc work: 0.8297 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2423 6942 5.085 %
Rwork0.2074 129590 -
all0.209 --
obs-136532 99.912 %
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: 41.337 Å2
Baniso -1Baniso -2Baniso -3
1--0.871 Å2-0.436 Å20 Å2
2---0.871 Å2-0 Å2
3---2.826 Å2
Refinement stepCycle: LAST / Resolution: 1.83→45.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 24 340 8290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138212
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157245
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.64311182
X-RAY DIFFRACTIONr_angle_other_deg1.3921.57916605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2885976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15921.184490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.339151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6951563
X-RAY DIFFRACTIONr_chiral_restr0.080.2977
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029489
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022141
X-RAY DIFFRACTIONr_nbd_refined0.2080.21611
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.26876
X-RAY DIFFRACTIONr_nbtor_refined0.180.23867
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2349
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.213
X-RAY DIFFRACTIONr_nbd_other0.1520.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.213
X-RAY DIFFRACTIONr_mcbond_it3.6854.2893910
X-RAY DIFFRACTIONr_mcbond_other3.6754.2883909
X-RAY DIFFRACTIONr_mcangle_it4.616.4234884
X-RAY DIFFRACTIONr_mcangle_other4.616.4244885
X-RAY DIFFRACTIONr_scbond_it4.014.5414302
X-RAY DIFFRACTIONr_scbond_other4.014.5414303
X-RAY DIFFRACTIONr_scangle_it5.4166.6926298
X-RAY DIFFRACTIONr_scangle_other5.4156.6926299
X-RAY DIFFRACTIONr_lrange_it6.45348.0829377
X-RAY DIFFRACTIONr_lrange_other6.43747.9739322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.8780.3925030.389527X-RAY DIFFRACTION99.801
1.878-1.9290.3765310.3589249X-RAY DIFFRACTION99.9898
1.929-1.9850.3874440.3319065X-RAY DIFFRACTION100
1.985-2.0460.3464690.3068770X-RAY DIFFRACTION100
2.046-2.1130.3294520.2818491X-RAY DIFFRACTION100
2.113-2.1870.3094500.2618266X-RAY DIFFRACTION100
2.187-2.270.2684650.2437928X-RAY DIFFRACTION100
2.27-2.3620.3054120.2527659X-RAY DIFFRACTION100
2.362-2.4670.2893970.2257324X-RAY DIFFRACTION99.987
2.467-2.5880.2654080.2257015X-RAY DIFFRACTION100
2.588-2.7280.2563580.226670X-RAY DIFFRACTION99.1255
2.728-2.8930.2543240.2086345X-RAY DIFFRACTION100
2.893-3.0930.2512890.2125987X-RAY DIFFRACTION100
3.093-3.340.2432730.2175580X-RAY DIFFRACTION100
3.34-3.6590.252550.2135157X-RAY DIFFRACTION100
3.659-4.0910.2092380.1864670X-RAY DIFFRACTION99.9796
4.091-4.7230.1842270.1464116X-RAY DIFFRACTION100
4.723-5.7830.191940.1633480X-RAY DIFFRACTION99.351
5.783-8.1720.1821610.162729X-RAY DIFFRACTION100
8.172-45.4190.214920.1671562X-RAY DIFFRACTION99.3393

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