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- PDB-24ai: alpha-1,2-glucosidase from Arthrobacter humicola A8F5, kojibiose ... -

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Basic information

Entry
Database: PDB / ID: 24ai
Titlealpha-1,2-glucosidase from Arthrobacter humicola A8F5, kojibiose complex
Componentsalpha-1,2-glucosidase
KeywordsHYDROLASE / glycoside hydrolase family 176
Function / homologyTRIETHYLENE GLYCOL / S-1,2-PROPANEDIOL
Function and homology information
Biological speciesArthrobacter humicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsYasukochi, R. / Fushinobu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Discovery and structural analysis of glycoside hydrolase family 176 alpha-1,2 glucosidase from Arthrobacter humicola A8F5.
Authors: Yasukochi, R. / Suzuki, T. / Toraya, T. / Hino, K. / Mori, T. / Kashima, T. / Miyanaga, A. / Watanabe, H. / Fushinobu, S.
History
DepositionFeb 26, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-1,2-glucosidase
B: alpha-1,2-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,40515
Polymers135,7312
Non-polymers1,67413
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint36 kcal/mol
Surface area42160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.784, 109.457, 105.372
Angle α, β, γ (deg.)90.00, 93.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein alpha-1,2-glucosidase


Mass: 67865.461 Da / Num. of mol.: 2 / Mutation: D427N
Source method: isolated from a genetically manipulated source
Details: Residues 33-58 of the original protein sequence were replaced with GGS.
Source: (gene. exp.) Arthrobacter humicola (bacteria) / Strain: A8F5 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CondonPlus-RIL
#2: Polysaccharide alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-2DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 394 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.1 M Sodium acetate pH5.1, 34%(v/v)1,2-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2025
RadiationMonochromator: liquid nitrogen cooled Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→49.64 Å / Num. obs: 119031 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.226 / Rrim(I) all: 0.237 / Net I/σ(I): 14.21
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.495 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 18995 / CC1/2: 0.796 / Rrim(I) all: 1.571 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.79→48.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.504 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20992 5850 4.9 %RANDOM
Rwork0.16839 ---
obs0.17045 112849 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.552 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20.04 Å2
2---0.01 Å20 Å2
3----1.49 Å2
Refinement stepCycle: 1 / Resolution: 1.79→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9214 0 111 383 9708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0129552
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168933
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.81213005
X-RAY DIFFRACTIONr_angle_other_deg0.7651.73720491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90251220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.32598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.219101345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.21421
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022272
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6372.5054901
X-RAY DIFFRACTIONr_mcbond_other3.6372.5054901
X-RAY DIFFRACTIONr_mcangle_it4.8794.4756114
X-RAY DIFFRACTIONr_mcangle_other4.8794.4766115
X-RAY DIFFRACTIONr_scbond_it4.7912.9634651
X-RAY DIFFRACTIONr_scbond_other4.792.9634652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7775.2096892
X-RAY DIFFRACTIONr_long_range_B_refined8.21524.8410059
X-RAY DIFFRACTIONr_long_range_B_other8.21424.8410060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 426 -
Rwork0.292 8318 -
obs--100 %

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