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- PDB-8yie: Crystal structure of GH13_30 alpha-glucosidase CmmB in complex wi... -

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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


oligosaccharide catabolic process / alpha-amylase activity
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.14 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)

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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 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

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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

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