[English] 日本語
Yorodumi
- PDB-24az: alpha-1,2-glucosidase from Arthrobacter humicola A8F5, kojitriose... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 24az
Titlealpha-1,2-glucosidase from Arthrobacter humicola A8F5, kojitriose complex
Componentsalpha-1,2-glucosidase
KeywordsHYDROLASE / glycoside hydrolase family 176
Function / homologyACETATE ION / S-1,2-PROPANEDIOL
Function and homology information
Biological speciesArthrobacter humicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)137,37114
Polymers135,7312
Non-polymers1,64112
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint44 kcal/mol
Surface area41320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.385, 107.985, 105.522
Angle α, β, γ (deg.)90.00, 93.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
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-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-2DGlcpa1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][a-D-Glcp]{[(2+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 151 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48 %
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

-
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: Dec 3, 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: 1.83→48.49 Å / Num. obs: 111405 / % possible obs: 99.8 % / Redundancy: 14.1 % / Biso Wilson estimate: 28.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.267 / Rrim(I) all: 0.277 / Net I/σ(I): 7.8
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 14.3 % / Rmerge(I) obs: 3.16 / Mean I/σ(I) obs: 1 / Num. unique obs: 5305 / CC1/2: 0.567 / Rrim(I) all: 3.277 / % possible all: 96.9

-
Processing

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

Resolution: 1.83→48.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.234 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 5479 4.9 %RANDOM
Rwork0.21046 ---
obs0.21272 105886 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.594 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å2-0 Å2-0.58 Å2
2---0.14 Å20 Å2
3----2.5 Å2
Refinement stepCycle: 1 / Resolution: 1.83→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9162 0 109 141 9412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0129499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168864
X-RAY DIFFRACTIONr_angle_refined_deg2.3371.81212948
X-RAY DIFFRACTIONr_angle_other_deg0.8121.73620332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.78851215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.326596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.596101334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022257
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_it4.6553.3554882
X-RAY DIFFRACTIONr_mcbond_other4.6443.3554881
X-RAY DIFFRACTIONr_mcangle_it6.2386.0016089
X-RAY DIFFRACTIONr_mcangle_other6.2386.0036090
X-RAY DIFFRACTIONr_scbond_it5.4853.7784617
X-RAY DIFFRACTIONr_scbond_other5.4843.7794618
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5396.7296860
X-RAY DIFFRACTIONr_long_range_B_refined9.40332.5410219
X-RAY DIFFRACTIONr_long_range_B_other9.40332.5510215
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.874 Å
RfactorNum. reflection% reflection
Rfree0.337 426 -
Rwork0.345 7612 -
obs--98.22 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more