[English] 日本語
Yorodumi
- PDB-8yie: Crystal structure of GH13_30 alpha-glucosidase CmmB in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yie
TitleCrystal structure of GH13_30 alpha-glucosidase CmmB in complex with acarbose
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / alpha-glucosidase / inhibitor / complex
Function / homology
Function and homology information


alpha-amylase activity / oligosaccharide catabolic process
Similarity search - Function
Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-acarbose / Alpha-glucosidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSaburi, W. / Tagami, T. / Yu, J. / Ose, T. / Yao, M. / Mori, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Food Biosci / Year: 2024
Title: Molecular mechanism for the substrate specificity of Arthrobacter globiformis M6 alpha-glucosidase CmmB, belonging to glycoside hydrolase family 13 subfamily 30
Authors: Saburi, W. / Tagami, T. / Usui, T. / Yu, J. / Ose, T. / Yao, M. / Mori, H.
History
DepositionFeb 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-glucosidase
B: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5054
Polymers122,2142
Non-polymers1,2912
Water18,9701053
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-5 kcal/mol
Surface area39190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.364, 66.190, 148.060
Angle α, β, γ (deg.)90.00, 95.74, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Alpha-glucosidase


Mass: 61106.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The residues which are missing in the molecule are not visible due to poor electron density.
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: cmmB / Production host: Escherichia coli (E. coli) / References: UniProt: D2YYD7, alpha-glucosidase
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp4Gc]{[(4+1)][<C2O2>]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1053 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5 mM acarbose, 0.1 M lithium acetate, 10% (w/v) polyethylene glycol 3400, and 5 mM HEPES-NaOH buffer (pH 7.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 107839 / % possible obs: 99.5 % / Redundancy: 3.37 % / CC1/2: 0.997 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.81 Å / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 17080 / CC1/2: 0.723 / Rrim(I) all: 0.672

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.7→49.11 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 1981 1.84 %
Rwork0.1646 --
obs0.1653 107830 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8213 0 88 1053 9354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d5.7361155
X-RAY DIFFRACTIONf_chiral_restr0.0561212
X-RAY DIFFRACTIONf_plane_restr0.0081549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.28011420.2337266X-RAY DIFFRACTION96
1.74-1.790.24351370.21827498X-RAY DIFFRACTION100
1.79-1.840.26251460.20597572X-RAY DIFFRACTION100
1.84-1.90.25451280.19497611X-RAY DIFFRACTION100
1.9-1.970.22441530.19167526X-RAY DIFFRACTION100
1.97-2.050.20231350.17217560X-RAY DIFFRACTION100
2.05-2.140.22151400.16377571X-RAY DIFFRACTION100
2.14-2.260.22851440.16327528X-RAY DIFFRACTION100
2.26-2.40.21471410.16217569X-RAY DIFFRACTION100
2.4-2.580.21251380.16717595X-RAY DIFFRACTION100
2.58-2.840.21061500.16477612X-RAY DIFFRACTION100
2.84-3.260.19851430.15857569X-RAY DIFFRACTION100
3.26-4.10.17521440.14017580X-RAY DIFFRACTION99
4.1-49.110.16141400.15217792X-RAY DIFFRACTION100

+
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