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- PDB-24il: alpha-1,2-glucosidase from Arthrobacter humicola A8F5, selaginose... -

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Basic information

Entry
Database: PDB / ID: 24il
Titlealpha-1,2-glucosidase from Arthrobacter humicola A8F5, selaginose complex
Componentsalpha-1,2-glucosidase from Arthrobacter humicola A8F5
KeywordsHYDROLASE / glycoside hydrolase family 176
Biological speciesArthrobacter humicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionMar 4, 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 from Arthrobacter humicola A8F5
B: alpha-1,2-glucosidase from Arthrobacter humicola A8F5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,23612
Polymers135,7312
Non-polymers1,50510
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint35 kcal/mol
Surface area41600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.803, 108.080, 105.435
Angle α, β, γ (deg.)90.00, 93.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alpha-1,2-glucosidase from Arthrobacter humicola A8F5


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 / References: kojibiose hydrolase
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-1DGlcpa1-2DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a1-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{[(2+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.5 %
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: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 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: 1.8→49.52 Å / Num. obs: 114361 / % possible obs: 99.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.054 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5627 / CC1/2: 0.848 / Rrim(I) all: 0.613 / % possible all: 99.7

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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: 1.8→48.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.32 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23985 5603 4.9 %RANDOM
Rwork0.19941 ---
obs0.20138 108701 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.361 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å2-0 Å20.15 Å2
2--0.33 Å20 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9231 0 100 204 9535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0129567
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168919
X-RAY DIFFRACTIONr_angle_refined_deg2.3051.81313048
X-RAY DIFFRACTIONr_angle_other_deg0.7951.73520469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17751227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.968597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.219101342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.21434
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022268
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_it4.3693.3594923
X-RAY DIFFRACTIONr_mcbond_other4.3683.3594923
X-RAY DIFFRACTIONr_mcangle_it5.9386.0126145
X-RAY DIFFRACTIONr_mcangle_other5.9396.0136146
X-RAY DIFFRACTIONr_scbond_it5.1583.7444644
X-RAY DIFFRACTIONr_scbond_other5.1583.7444645
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.056.6986904
X-RAY DIFFRACTIONr_long_range_B_refined8.86932.3710249
X-RAY DIFFRACTIONr_long_range_B_other8.86732.3710249
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 440 -
Rwork0.273 8043 -
obs--99.69 %

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