[English] 日本語
Yorodumi
- PDB-9izo: Apg mutant enzyme D336A of acarbose hydrolase from human gut flor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9izo
TitleApg mutant enzyme D336A of acarbose hydrolase from human gut flora K. grimontii TD1, complex with acarviosine
ComponentsMaltodextrin glucosidase
KeywordsHYDROLASE / Complex
Function / homology
Function and homology information


neopullulanase activity / neopullulanase / alpha-1,4-glucosidase activity / alpha-glucosidase / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Maltodextrin glucosidase / Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Maltodextrin glucosidase
Similarity search - Component
Biological speciesKlebsiella grimontii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsZhou, J.H. / Huang, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Molecular insights of acarbose metabolization catalyzed by acarbose-preferred glucosidase.
Authors: Huang, J. / Shen, Z. / Xiao, X. / Wang, L. / Zhang, J. / Zhou, J. / Gu, Y.
History
DepositionAug 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltodextrin glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3862
Polymers69,0651
Non-polymers3211
Water5,188288
1
A: Maltodextrin glucosidase
hetero molecules

A: Maltodextrin glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,7724
Polymers138,1292
Non-polymers6432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area4310 Å2
ΔGint-4 kcal/mol
Surface area42560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.510, 75.510, 399.409
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

-
Components

#1: Protein Maltodextrin glucosidase / Apg


Mass: 69064.633 Da / Num. of mol.: 1 / Mutation: D336A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella grimontii (bacteria) / Gene: tvaI, malZ, HV064_03130, NCTC9149_05459 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A7H4P971, neopullulanase, alpha-glucosidase
#2: Sugar ChemComp-A1EAX / (2~{S},3~{R},4~{S},5~{R},6~{R})-5-[[(1~{S},4~{R},5~{S},6~{S})-3-(hydroxymethyl)-4,5,6-tris(oxidanyl)cyclohex-2-en-1-yl]amino]-6-methyl-oxane-2,3,4-triol


Type: D-saccharide, alpha linking / Mass: 321.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H23NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES,PH 7.5 2.0 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.13→46.66 Å / Num. obs: 39402 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 31.99 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.8
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3126 / CC1/2: 0.887 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VT9

7vt9


Resolution: 2.13→46.65 Å / SU ML: 0.2659 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 1925 4.91 %
Rwork0.2086 37261 -
obs0.2106 39186 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.04 Å2
Refinement stepCycle: LAST / Resolution: 2.13→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 22 288 5030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784886
X-RAY DIFFRACTIONf_angle_d0.95946649
X-RAY DIFFRACTIONf_chiral_restr0.0705681
X-RAY DIFFRACTIONf_plane_restr0.0075873
X-RAY DIFFRACTIONf_dihedral_angle_d14.19091759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.180.30541200.27412585X-RAY DIFFRACTION99.59
2.18-2.240.34051350.25062569X-RAY DIFFRACTION99.48
2.24-2.310.33751230.24752602X-RAY DIFFRACTION99.49
2.31-2.380.32771340.24192613X-RAY DIFFRACTION99.6
2.38-2.470.30221640.22942571X-RAY DIFFRACTION99.67
2.47-2.570.26881310.23082608X-RAY DIFFRACTION99.75
2.57-2.680.29331370.22442617X-RAY DIFFRACTION99.75
2.68-2.820.28161520.22492604X-RAY DIFFRACTION99.82
2.82-30.25481450.2222662X-RAY DIFFRACTION99.93
3-3.230.25161300.22352654X-RAY DIFFRACTION99.82
3.23-3.560.25481440.20072672X-RAY DIFFRACTION99.86
3.56-4.070.20481470.18372708X-RAY DIFFRACTION99.96
4.07-5.130.18321210.16972795X-RAY DIFFRACTION99.93
5.13-46.650.23881420.2113001X-RAY DIFFRACTION99.59

+
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