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- PDB-3wy2: Crystal structure of alpha-glucosidase in complex with glucose -

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Basic information

Entry
Database: PDB / ID: 3wy2
TitleCrystal structure of alpha-glucosidase in complex with glucose
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / alpha-glucosidase / TIM barrel / glucosidase / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


: / alpha-glucosidase / oligosaccharide catabolic process / alpha-amylase activity / metal ion binding
Similarity search - Function
Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Alpha-glucosidase
Similarity search - Component
Biological speciesHalomonas sp. H11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.471 Å
AuthorsShen, X. / Gai, Z. / Kato, K. / Yao, M.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Structural analysis of the alpha-glucosidase HaG provides new insights into substrate specificity and catalytic mechanism
Authors: Shen, X. / Saburi, W. / Gai, Z. / Kato, K. / Ojima-Kato, T. / Yu, J. / Komoda, K. / Kido, Y. / Matsui, H. / Mori, H. / Yao, M.
History
DepositionAug 18, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-glucosidase
B: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,13511
Polymers122,3542
Non-polymers7819
Water27,0771503
1
A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7507
Polymers61,1771
Non-polymers5736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3864
Polymers61,1771
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.219, 103.809, 176.890
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 Alpha-glucosidase


Mass: 61177.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas sp. H11 (bacteria) / Gene: aglA / Plasmid: pFLAG-CTS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H3K096, alpha-glucosidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-BGC / beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1503 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG 6000, 0.1M HEPES, 0.5M lithium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 10, 2013 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. all: 197498 / Num. obs: 197034 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.47-1.567.20.5393.931207198.9
1.56-1.677.30.3416.2298041100
1.67-1.87.40.20710277211100
1.8-1.977.40.11617.1255841100
1.97-2.217.40.06528.623203199.9
2.21-2.557.40.04340.6205551100
2.55-3.127.30.03252.9174631100
3.12-4.47.20.02470.113650199.9
4.4-506.60.02373.77847199.5

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.471→46.085 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1791 9848 5 %
Rwork0.1562 187179 -
obs0.1574 197027 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.95 Å2 / Biso mean: 19.9211 Å2 / Biso min: 7.05 Å2
Refinement stepCycle: LAST / Resolution: 1.471→46.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8584 0 49 1503 10136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018902
X-RAY DIFFRACTIONf_angle_d1.0612133
X-RAY DIFFRACTIONf_chiral_restr0.0731258
X-RAY DIFFRACTIONf_plane_restr0.0061610
X-RAY DIFFRACTIONf_dihedral_angle_d12.8433225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4709-1.48760.29443050.23725845615095
1.4876-1.50510.23233270.204662096536100
1.5051-1.52350.22393240.198461516475100
1.5235-1.54270.24013290.1962626591100
1.5427-1.5630.19953240.181461316455100
1.563-1.58450.20763260.180561916517100
1.5845-1.60710.21243250.178861786503100
1.6071-1.63110.20893280.167462296557100
1.6311-1.65660.19573250.163461816506100
1.6566-1.68370.20053270.162162126539100
1.6837-1.71280.17773270.158262226549100
1.7128-1.74390.17293260.159661836509100
1.7439-1.77750.20863190.169362096528100
1.7775-1.81370.19013290.164862496578100
1.8137-1.85320.19983240.161662176541100
1.8532-1.89630.19773520.159361966548100
1.8963-1.94370.18753380.159861856523100
1.9437-1.99630.18373180.155262796597100
1.9963-2.0550.19423220.152662296551100
2.055-2.12130.16633170.155662426559100
2.1213-2.19720.17593210.154462386559100
2.1972-2.28510.16833300.156462606590100
2.2851-2.38910.1823380.155762656603100
2.3891-2.51510.17873350.161562736608100
2.5151-2.67260.18723270.158962966623100
2.6726-2.8790.1713310.162763156646100
2.879-3.16860.1913190.15563486667100
3.1686-3.6270.15413390.14363306669100
3.627-4.56890.14273540.127164076761100
4.5689-46.10780.17143420.149466476989100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4239-0.0368-0.13710.18750.07080.65430.02850.02930.00010.0027-0.03390.0095-0.0232-0.06730.00840.07290.00580.00240.0727-0.01460.0973-40.825812.2212-17.8267
20.4191-0.18720.43720.3365-0.27141.1411-0.0633-0.00510.09120.0577-0.0126-0.0504-0.11230.00720.0270.10770.0279-0.01380.0806-0.01710.1225-15.8766-15.15822.5761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA4 - 538
2X-RAY DIFFRACTION2CHAIN BB4 - 538

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