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- PDB-8ids: Crystal structure of Bacillus sp. AHU2216 GH13_31 Alpha-glucosida... -

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Basic information

Entry
Database: PDB / ID: 8ids
TitleCrystal structure of Bacillus sp. AHU2216 GH13_31 Alpha-glucosidase E256Q/N258P in complex with maltotriose
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / alpha-glucosidase / GH13_31 / alpha-amylase / maltotriose
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 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-maltotriose / Alpha-glucosidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAuiewiriyanukul, W. / Saburi, W. / Yu, J. / Kato, K. / Yao, M. / Mori, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2023
Title: Alteration of Substrate Specificity and Transglucosylation Activity of GH13_31 alpha-Glucosidase from Bacillus sp. AHU2216 through Site-Directed Mutagenesis of Asn258 on beta → alpha Loop 5.
Authors: Auiewiriyanukul, W. / Saburi, W. / Ota, T. / Yu, J. / Kato, K. / Yao, M. / Mori, H.
History
DepositionFeb 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5674
Polymers65,9831
Non-polymers5853
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.517, 89.202, 128.282
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: 65982.625 Da / Num. of mol.: 1 / Mutation: E256Q,N258P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (in: firmicutes) (bacteria)
Gene: BspAG13A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z5WH92
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 mM maltotetraose, 0.2 M calcium chloride, and 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 104555 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rrim(I) all: 0.088 / Net I/σ(I): 19.71
Reflection shellResolution: 1.5→1.59 Å / Mean I/σ(I) obs: 2.76 / Num. unique obs: 16645 / CC1/2: 0.851 / Rrim(I) all: 0.835 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→47.74 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1859 5229 5 %
Rwork0.1645 --
obs0.1656 104545 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 36 545 5053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016
X-RAY DIFFRACTIONf_angle_d1.406
X-RAY DIFFRACTIONf_dihedral_angle_d7.038611
X-RAY DIFFRACTIONf_chiral_restr0.115651
X-RAY DIFFRACTIONf_plane_restr0.011807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.25091690.21173215X-RAY DIFFRACTION98
1.52-1.530.25781730.19633283X-RAY DIFFRACTION100
1.53-1.550.2221720.18973262X-RAY DIFFRACTION100
1.55-1.570.2211720.1833269X-RAY DIFFRACTION100
1.57-1.590.17951730.16793290X-RAY DIFFRACTION100
1.59-1.610.20321730.17033288X-RAY DIFFRACTION100
1.61-1.640.21561700.17653229X-RAY DIFFRACTION100
1.64-1.660.19291750.18323324X-RAY DIFFRACTION100
1.66-1.690.19941720.18293258X-RAY DIFFRACTION100
1.69-1.720.24731710.19693315X-RAY DIFFRACTION100
1.72-1.750.23471760.21363256X-RAY DIFFRACTION100
1.75-1.780.24341740.20073277X-RAY DIFFRACTION100
1.78-1.810.2181660.17563281X-RAY DIFFRACTION100
1.81-1.850.19531890.16213281X-RAY DIFFRACTION100
1.85-1.890.17741740.16183332X-RAY DIFFRACTION100
1.89-1.930.18771690.1553255X-RAY DIFFRACTION100
1.93-1.980.18211660.15743298X-RAY DIFFRACTION100
1.98-2.030.19031750.16543323X-RAY DIFFRACTION100
2.03-2.090.18461840.16123284X-RAY DIFFRACTION100
2.09-2.160.17741840.1663282X-RAY DIFFRACTION100
2.16-2.240.19871580.16173329X-RAY DIFFRACTION100
2.24-2.330.17251680.16093311X-RAY DIFFRACTION100
2.33-2.430.20571750.15843339X-RAY DIFFRACTION100
2.43-2.560.17031710.16713349X-RAY DIFFRACTION100
2.56-2.720.19521930.16713287X-RAY DIFFRACTION100
2.72-2.930.19521660.17193369X-RAY DIFFRACTION100
2.93-3.230.19971770.16493343X-RAY DIFFRACTION100
3.23-3.70.14981790.15643394X-RAY DIFFRACTION100
3.7-4.660.1331790.13453419X-RAY DIFFRACTION100
4.66-47.740.20351860.16983574X-RAY DIFFRACTION100

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