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

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Basic information

Entry
Database: PDB / ID: 8yif
TitleCrystal structure of GH13_30 alpha-glucosidase CmmB in complex with acarviosin
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-glucosidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4982
Polymers64,1621
Non-polymers3351
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.223, 73.336, 73.213
Angle α, β, γ (deg.)90.00, 90.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-glucosidase


Mass: 64162.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BAI67603.1 / Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: cmmB / Production host: Escherichia coli (E. coli) / References: UniProt: D2YYD7
#2: Chemical ChemComp-A1L2I / Acarviosin / (1~{S},2~{S},3~{R},6~{S})-4-(hydroxymethyl)-6-[[(2~{R},3~{S},4~{S},5~{R},6~{S})-6-methoxy-2-methyl-4,5-bis(oxidanyl)oxan-3-yl]amino]cyclohex-4-ene-1,2,3-triol


Mass: 335.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H25NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 42.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5 mM acarviosin, 0.5 M lithium chloride, 10% (w/v) polyethylene glycol 6000, and 55 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: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 70932 / % possible obs: 99.6 % / Redundancy: 6.61 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.089 / Net I/σ(I): 15.7
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 11229 / CC1/2: 0.873 / Rrim(I) all: 0.731

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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: 8YIE

8yie


Resolution: 1.6→42.13 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 1992 2.81 %
Rwork0.1706 --
obs0.1713 70926 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 23 425 4680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.827
X-RAY DIFFRACTIONf_dihedral_angle_d5.75598
X-RAY DIFFRACTIONf_chiral_restr0.054614
X-RAY DIFFRACTIONf_plane_restr0.01800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28771370.25874711X-RAY DIFFRACTION97
1.64-1.690.23061370.21744919X-RAY DIFFRACTION99
1.69-1.740.25891370.19664883X-RAY DIFFRACTION99
1.74-1.790.2341420.18054923X-RAY DIFFRACTION100
1.79-1.860.21411430.17834901X-RAY DIFFRACTION100
1.86-1.930.20631400.17474925X-RAY DIFFRACTION100
1.93-2.020.20051410.17744907X-RAY DIFFRACTION100
2.02-2.120.20951450.1694946X-RAY DIFFRACTION100
2.12-2.260.20341460.16744929X-RAY DIFFRACTION100
2.26-2.430.19031450.1674947X-RAY DIFFRACTION100
2.43-2.680.19571420.17534950X-RAY DIFFRACTION100
2.68-3.060.16881450.184965X-RAY DIFFRACTION100
3.06-3.860.181470.16014980X-RAY DIFFRACTION100

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