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- PDB-5zce: Crystal structure of Alpha-glucosidase in complex with maltotetraose -

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Basic information

Entry
Database: PDB / ID: 5zce
TitleCrystal structure of Alpha-glucosidase in complex with maltotetraose
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-maltotetraose / Alpha-glucosidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.555 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 / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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)65,7155
Polymers64,9281
Non-polymers7874
Water14,718817
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-19 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.989, 84.549, 128.715
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-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][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.: 817 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
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: 1.56→50 Å / Num. obs: 84637 / % possible obs: 97.4 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.117 / Net I/σ(I): 11.7
Reflection shellResolution: 1.56→1.65 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 13136 / Rrim(I) all: 0.773 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZE0

2ze0


Resolution: 1.555→46.097 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 4232 5 %
Rwork0.1721 --
obs0.1731 84632 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.555→46.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 48 817 5359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064663
X-RAY DIFFRACTIONf_angle_d0.96321
X-RAY DIFFRACTIONf_dihedral_angle_d3.4372753
X-RAY DIFFRACTIONf_chiral_restr0.055660
X-RAY DIFFRACTIONf_plane_restr0.005810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5553-1.5730.28171310.25562501X-RAY DIFFRACTION91
1.573-1.59150.28581330.24492527X-RAY DIFFRACTION95
1.5915-1.61090.21291380.232614X-RAY DIFFRACTION96
1.6109-1.63130.26291370.22242611X-RAY DIFFRACTION96
1.6313-1.65270.26891380.21122612X-RAY DIFFRACTION96
1.6527-1.67540.22271380.20562618X-RAY DIFFRACTION96
1.6754-1.69930.21431370.19522607X-RAY DIFFRACTION96
1.6993-1.72470.22871390.19452635X-RAY DIFFRACTION97
1.7247-1.75160.22861370.19642614X-RAY DIFFRACTION96
1.7516-1.78040.20091400.19762648X-RAY DIFFRACTION97
1.7804-1.81110.18251370.18942604X-RAY DIFFRACTION97
1.8111-1.8440.19661410.18372683X-RAY DIFFRACTION97
1.844-1.87950.22721400.17432664X-RAY DIFFRACTION97
1.8795-1.91780.1881390.17112641X-RAY DIFFRACTION97
1.9178-1.95950.17261410.17152679X-RAY DIFFRACTION98
1.9595-2.00510.19431390.17442648X-RAY DIFFRACTION98
2.0051-2.05520.20291430.16582703X-RAY DIFFRACTION98
2.0552-2.11080.18571410.16832682X-RAY DIFFRACTION98
2.1108-2.17290.19761410.16612682X-RAY DIFFRACTION98
2.1729-2.24310.19431420.17022695X-RAY DIFFRACTION98
2.2431-2.32320.19441410.16692687X-RAY DIFFRACTION98
2.3232-2.41620.20861440.16762730X-RAY DIFFRACTION98
2.4162-2.52620.19321430.16782711X-RAY DIFFRACTION98
2.5262-2.65940.19571440.16722748X-RAY DIFFRACTION99
2.6594-2.8260.16771440.17272732X-RAY DIFFRACTION99
2.826-3.04410.16351460.16672762X-RAY DIFFRACTION99
3.0441-3.35040.18531440.16762753X-RAY DIFFRACTION99
3.3504-3.8350.1741480.15512798X-RAY DIFFRACTION99
3.835-4.83090.16661490.14032846X-RAY DIFFRACTION100
4.8309-46.11740.18871570.17892965X-RAY DIFFRACTION99

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