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- PDB-5djw: Crystal structure of Family 31 alpha-glucosidase (BT_3299) from B... -

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Basic information

Entry
Database: PDB / ID: 5djw
TitleCrystal structure of Family 31 alpha-glucosidase (BT_3299) from Bacteroides thetaiotaomicron
ComponentsAlpha-glucosidase II
KeywordsCarbohydrate Binding Protein / Family Glycoside Hydrolase 31 / alpha-glucosidase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Alpha-glucosidase II
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsChaudet, M.M. / Rose, D.R.
CitationJournal: Biochem.Cell Biol. / Year: 2016
Title: Suggested alternative starch utilization system from the human gut bacterium Bacteroides thetaiotaomicron.
Authors: Chaudet, M.M. / Rose, D.R.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-glucosidase II
B: Alpha-glucosidase II


Theoretical massNumber of molelcules
Total (without water)155,9372
Polymers155,9372
Non-polymers00
Water41423
1
A: Alpha-glucosidase II


Theoretical massNumber of molelcules
Total (without water)77,9681
Polymers77,9681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-glucosidase II


Theoretical massNumber of molelcules
Total (without water)77,9681
Polymers77,9681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.260, 74.860, 94.430
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-glucosidase II


Mass: 77968.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3299 / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A2K6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Ammonium Sulfate, 0.05 M Bis-Tris:HCl pH 6.5 30% (v/v), Pentaerythritol Ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→47.55 Å / Num. obs: 34303 / % possible obs: 99.9 % / Redundancy: 7.6 % / Net I/σ(I): 4.79
Reflection shellResolution: 2.7→2.797 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHENIX1.9_1692phasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7→47.55 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 44.73 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3897 1716 5 %Random selection
Rwork0.3299 ---
obs0.3329 34299 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9118 0 0 23 9141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099660
X-RAY DIFFRACTIONf_angle_d1.71913103
X-RAY DIFFRACTIONf_dihedral_angle_d17.2723476
X-RAY DIFFRACTIONf_chiral_restr0.0811374
X-RAY DIFFRACTIONf_plane_restr0.0081704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.77950.45481430.37132718X-RAY DIFFRACTION100
2.7795-2.86920.47921410.36912678X-RAY DIFFRACTION100
2.8692-2.97170.41981420.34712680X-RAY DIFFRACTION100
2.9717-3.09070.43231430.35282717X-RAY DIFFRACTION100
3.0907-3.23130.38821420.34922700X-RAY DIFFRACTION100
3.2313-3.40160.40551420.34052708X-RAY DIFFRACTION100
3.4016-3.61470.39721420.34242696X-RAY DIFFRACTION100
3.6147-3.89360.43031430.31832723X-RAY DIFFRACTION100
3.8936-4.28530.38191420.31012698X-RAY DIFFRACTION100
4.2853-4.90480.36641430.30052705X-RAY DIFFRACTION100
4.9048-6.17740.30111450.32582755X-RAY DIFFRACTION100
6.1774-47.550.38961480.32672805X-RAY DIFFRACTION100

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