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- PDB-5zcd: Crystal structure of Alpha-glucosidase in complex with maltotriose -

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Basic information

Entry
Database: PDB / ID: 5zcd
TitleCrystal structure of Alpha-glucosidase in complex with maltotriose
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / Alpha-glucosidase
Function / homology
Function and homology information


alpha-amylase activity / oligosaccharide catabolic process / metal ion binding
Similarity search - Function
Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / 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 / Glycosidases / Glycoside hydrolase superfamily ...Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / Alpha-glucosidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.707 Å
AuthorsKato, K. / Saburi, W. / Yao, M.
CitationJournal: FEBS Lett. / Year: 2018
Title: Function and structure of GH13_31 alpha-glucosidase with high alpha-(1→4)-glucosidic linkage specificity and transglucosylation activity.
Authors: Auiewiriyanukul, W. / Saburi, W. / Kato, K. / Yao, M. / Mori, H.
History
DepositionFeb 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: 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 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5535
Polymers64,9281
Non-polymers6254
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.628, 84.745, 128.514
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: 64928.445 Da / Num. of mol.: 1 / Mutation: E256Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z5WH92*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350, Calcium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 66627 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.117 / Net I/σ(I): 11.1
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2 / Num. unique obs: 10452 / Rrim(I) all: 0.743 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZE0

2ze0


Resolution: 1.707→46.504 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.92
RfactorNum. reflection% reflection
Rfree0.2055 3335 5.01 %
Rwork0.1778 --
obs0.1792 66613 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.707→46.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 37 702 5233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064651
X-RAY DIFFRACTIONf_angle_d1.0416303
X-RAY DIFFRACTIONf_dihedral_angle_d13.0021722
X-RAY DIFFRACTIONf_chiral_restr0.042655
X-RAY DIFFRACTIONf_plane_restr0.005810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7066-1.73090.34441280.28472419X-RAY DIFFRACTION92
1.7309-1.75680.28881450.27222584X-RAY DIFFRACTION100
1.7568-1.78420.28351320.25982601X-RAY DIFFRACTION100
1.7842-1.81350.26951390.25022628X-RAY DIFFRACTION100
1.8135-1.84480.27631390.23362616X-RAY DIFFRACTION100
1.8448-1.87830.26241370.21832611X-RAY DIFFRACTION100
1.8783-1.91440.23011500.20282626X-RAY DIFFRACTION100
1.9144-1.95350.26291300.19752592X-RAY DIFFRACTION100
1.9535-1.9960.21881350.18912626X-RAY DIFFRACTION100
1.996-2.04240.19881360.18562611X-RAY DIFFRACTION100
2.0424-2.09350.22581450.17712608X-RAY DIFFRACTION100
2.0935-2.15010.21831350.18162659X-RAY DIFFRACTION100
2.1501-2.21340.22861330.18222617X-RAY DIFFRACTION100
2.2134-2.28480.22791400.17412628X-RAY DIFFRACTION100
2.2848-2.36650.20311410.17222636X-RAY DIFFRACTION100
2.3665-2.46120.23351330.17192644X-RAY DIFFRACTION100
2.4612-2.57320.20051490.17682632X-RAY DIFFRACTION100
2.5732-2.70890.19231370.182658X-RAY DIFFRACTION100
2.7089-2.87860.21271370.18162651X-RAY DIFFRACTION100
2.8786-3.10080.21591380.1772678X-RAY DIFFRACTION100
3.1008-3.41270.1891390.16872669X-RAY DIFFRACTION100
3.4127-3.90630.18281440.15662702X-RAY DIFFRACTION100
3.9063-4.92070.16791430.14212716X-RAY DIFFRACTION100
4.9207-46.52140.16551500.16542866X-RAY DIFFRACTION100

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