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- PDB-3wy3: Crystal structure of alpha-glucosidase mutant D202N in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3wy3
TitleCrystal structure of alpha-glucosidase mutant D202N in complex with glucose and glycerol
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / alpha-glucosidase / TIM barrel / glucosidase / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


alpha-glucosidase / glucan 1,4-alpha-maltotriohydrolase activity / oligo-1,6-glucosidase activity / maltose catabolic process / : / sucrose alpha-glucosidase activity / sucrose catabolic process / alpha-amylase activity / amino acid transport / 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: 3 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
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 / Database references ...Data collection / Database references / 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)123,12910
Polymers122,3522
Non-polymers7778
Water00
1
A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5655
Polymers61,1761
Non-polymers3894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5655
Polymers61,1761
Non-polymers3894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.530, 119.570, 177.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 4 - 538 / Label seq-ID: 4 - 538

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Alpha-glucosidase


Mass: 61176.086 Da / Num. of mol.: 2 / Mutation: D202N
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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
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

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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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% Polyacrylic acid 5100, 0.1M HEPES, 0.02M magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 14, 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: 3→50 Å / Num. all: 26809 / Num. obs: 26750 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3-3.187.40.5755.54210199
3.18-3.47.50.3638.439841100
3.4-3.677.50.24711.637171100
3.67-4.027.40.16715.534701100
4.02-4.497.40.11319.731461100
4.49-5.177.50.09422.327831100
5.17-6.327.30.0922.323961100
6.32-8.857.10.06726.81894199.9
8.85-506.50.04635.61150198.9

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1391)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→42.535 Å / FOM work R set: 0.7994 / SU ML: 0.34 / σ(F): 1.36 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1331 5 %RANDOM
Rwork0.198 ---
all0.2004 26809 --
obs0.2004 26642 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.06 Å2 / Biso mean: 42.09 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: LAST / Resolution: 3→42.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8584 0 50 0 8634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028894
X-RAY DIFFRACTIONf_angle_d0.66512120
X-RAY DIFFRACTIONf_chiral_restr0.0271262
X-RAY DIFFRACTIONf_plane_restr0.0041606
X-RAY DIFFRACTIONf_dihedral_angle_d12.6043222
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5131X-RAY DIFFRACTION5.139TORSIONAL
12B5131X-RAY DIFFRACTION5.139TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.10720.29851300.275124812611
3.1072-3.23160.32991320.265324932625
3.2316-3.37860.28231310.246925012632
3.3786-3.55660.29531300.242124902620
3.5566-3.77930.22731330.2125022635
3.7793-4.07090.25571310.18925072638
4.0709-4.48020.21341340.177525262660
4.4802-5.12750.22071330.156925352668
5.1275-6.45650.22781350.168225662701
6.4565-42.53960.19941420.172627102852

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