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- PDB-5i3d: Sulfolobus solfataricus beta-glycosidase - E387Y mutant -

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Basic information

Entry
Database: PDB / ID: 5i3d
TitleSulfolobus solfataricus beta-glycosidase - E387Y mutant
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Glycosidase
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...: / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Beta-galactosidase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsIglesias-Fernandez, J. / Hancock, S.M. / Lee, S.S. / McAuley, K.E. / Fordham-Skelton, A. / Rovira, C. / Davis, B.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: A front-face 'SNi synthase' engineered from a retaining 'double-SN2' hydrolase.
Authors: Iglesias-Fernandez, J. / Hancock, S.M. / Lee, S.S. / Khan, M. / Kirkpatrick, J. / Oldham, N.J. / McAuley, K. / Fordham-Skelton, A. / Rovira, C. / Davis, B.G.
History
DepositionFeb 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references / Source and taxonomy
Revision 1.2Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 25, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value
Revision 1.5Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)228,43020
Polymers227,1744
Non-polymers1,25616
Water18,3571019
1
B: Beta-galactosidase
D: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,43020
Polymers227,1744
Non-polymers1,25616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area13270 Å2
ΔGint-51 kcal/mol
Surface area65400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.680, 129.060, 191.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-galactosidase / Lactase


Mass: 56793.449 Da / Num. of mol.: 4 / Mutation: E387Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Gene: lacS, SSO3019
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P22498, beta-galactosidase
#2: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.25 / Details: PEG 4000, sodium acetate, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Sep 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.16→42.528 Å / Num. obs: 119882 / % possible obs: 97 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 11.2
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 61

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia20.4data reduction
Aimlessdata scaling
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GOW

1gow


Resolution: 2.16→42.528 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.92
RfactorNum. reflection% reflection
Rfree0.203 6001 5.01 %
Rwork0.1703 --
obs0.1719 119861 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.16→42.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15795 0 85 1019 16899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316381
X-RAY DIFFRACTIONf_angle_d0.63322253
X-RAY DIFFRACTIONf_dihedral_angle_d13.5089423
X-RAY DIFFRACTIONf_chiral_restr0.0452205
X-RAY DIFFRACTIONf_plane_restr0.0042900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.18450.32671140.25542370X-RAY DIFFRACTION61
2.1845-2.21020.27451300.25072334X-RAY DIFFRACTION60
2.2102-2.23720.30361740.23383308X-RAY DIFFRACTION86
2.2372-2.26550.25522020.22473919X-RAY DIFFRACTION100
2.2655-2.29530.27172030.22463822X-RAY DIFFRACTION100
2.2953-2.32680.26531940.22533895X-RAY DIFFRACTION100
2.3268-2.360.26092030.21813862X-RAY DIFFRACTION100
2.36-2.39520.25542050.20943905X-RAY DIFFRACTION100
2.3952-2.43260.261870.20573899X-RAY DIFFRACTION100
2.4326-2.47250.25122110.20263865X-RAY DIFFRACTION100
2.4725-2.51520.24492360.19543876X-RAY DIFFRACTION100
2.5152-2.56090.241850.19383900X-RAY DIFFRACTION100
2.5609-2.61010.23591990.18563856X-RAY DIFFRACTION100
2.6101-2.66340.22362300.19173902X-RAY DIFFRACTION100
2.6634-2.72130.22821810.18493908X-RAY DIFFRACTION100
2.7213-2.78460.23452010.18263903X-RAY DIFFRACTION100
2.7846-2.85420.21382180.18463879X-RAY DIFFRACTION100
2.8542-2.93140.21142040.18243909X-RAY DIFFRACTION100
2.9314-3.01760.21661880.18483914X-RAY DIFFRACTION100
3.0176-3.1150.2412030.18153923X-RAY DIFFRACTION100
3.115-3.22630.20712280.17923895X-RAY DIFFRACTION100
3.2263-3.35540.22952230.17823876X-RAY DIFFRACTION100
3.3554-3.50810.19942100.16193936X-RAY DIFFRACTION100
3.5081-3.69290.16972200.15183935X-RAY DIFFRACTION100
3.6929-3.92410.15532070.13993922X-RAY DIFFRACTION100
3.9241-4.22690.1722060.13613969X-RAY DIFFRACTION100
4.2269-4.65180.13982000.12293983X-RAY DIFFRACTION100
4.6518-5.32380.14831920.13114000X-RAY DIFFRACTION100
5.3238-6.70310.16222300.1514018X-RAY DIFFRACTION100
6.7031-100.16662170.14654177X-RAY DIFFRACTION99

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