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- PDB-5zcc: Crystal structure of Alpha-glucosidase in complex with maltose -

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Basic information

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


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 / 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-maltose / Alpha-glucosidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.704 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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.type / _entity.formula_weight / _entity.pdbx_description / _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)65,3915
Polymers64,9281
Non-polymers4634
Water14,772820
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 area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.046, 84.840, 128.767
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 / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][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.: 820 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
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: 66318 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.095 / Net I/σ(I): 13.9
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 10312 / Rrim(I) all: 0.656 / % possible all: 97

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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: 1.704→46.178 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.31
RfactorNum. reflection% reflection
Rfree0.1893 3323 5.01 %
Rwork0.1637 --
obs0.165 66310 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.704→46.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 26 820 5340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074639
X-RAY DIFFRACTIONf_angle_d1.0746285
X-RAY DIFFRACTIONf_dihedral_angle_d12.8971713
X-RAY DIFFRACTIONf_chiral_restr0.05650
X-RAY DIFFRACTIONf_plane_restr0.005810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7041-1.72850.23891240.22682296X-RAY DIFFRACTION88
1.7285-1.75430.25611340.22062583X-RAY DIFFRACTION100
1.7543-1.78170.24011440.21082613X-RAY DIFFRACTION100
1.7817-1.81090.21221330.20712596X-RAY DIFFRACTION100
1.8109-1.84210.24031420.19382634X-RAY DIFFRACTION100
1.8421-1.87560.24361340.1922577X-RAY DIFFRACTION100
1.8756-1.91170.24181360.18462619X-RAY DIFFRACTION100
1.9117-1.95070.21061430.17892615X-RAY DIFFRACTION100
1.9507-1.99320.21721340.17352590X-RAY DIFFRACTION100
1.9932-2.03950.1881380.16552640X-RAY DIFFRACTION100
2.0395-2.09050.19231370.16012577X-RAY DIFFRACTION100
2.0905-2.14710.17971360.16242633X-RAY DIFFRACTION100
2.1471-2.21020.21091430.16332626X-RAY DIFFRACTION100
2.2102-2.28160.19591360.16212621X-RAY DIFFRACTION100
2.2816-2.36310.20771340.16012612X-RAY DIFFRACTION100
2.3631-2.45770.18271410.15932642X-RAY DIFFRACTION100
2.4577-2.56960.18291390.16632642X-RAY DIFFRACTION100
2.5696-2.7050.17911380.15962626X-RAY DIFFRACTION100
2.705-2.87450.17591390.16722658X-RAY DIFFRACTION100
2.8745-3.09640.19611410.16572659X-RAY DIFFRACTION100
3.0964-3.40790.1941390.16092670X-RAY DIFFRACTION100
3.4079-3.90080.17341430.14622694X-RAY DIFFRACTION100
3.9008-4.91370.15981430.13652710X-RAY DIFFRACTION100
4.9137-46.19480.16931520.16532854X-RAY DIFFRACTION100

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