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- PDB-9ize: Acarbose hydrolase from human gut microbiota K. grimontii TD1, Ap... -

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Basic information

Entry
Database: PDB / ID: 9ize
TitleAcarbose hydrolase from human gut microbiota K. grimontii TD1, Apg mutant enzyme D336A, complexed with acarviosine-glucose
ComponentsMaltodextrin glucosidase
KeywordsHYDROLASE / Hydolase / 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: 1.87 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltodextrin glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5482
Polymers69,0651
Non-polymers4831
Water7,674426
1
A: Maltodextrin glucosidase
hetero molecules

A: Maltodextrin glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0964
Polymers138,1292
Non-polymers9672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area5070 Å2
ΔGint-1 kcal/mol
Surface area43320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.474, 75.474, 400.462
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 on special symmetry positions
IDModelComponents
11A-1014-

HOH

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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: Polysaccharide (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) ...(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-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 483.465 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
[][a-D-Glcp]{[(4+1)][a-D-Fucp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium chloride,0.1 M HEPES (pH 7.0),1.6 M ammonium sulfate

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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: Dec 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.87→46.7 Å / Num. obs: 57650 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 26.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.5
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3613 / CC1/2: 0.984 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VT9

7vt9


Resolution: 1.87→46.7 Å / SU ML: 0.2433 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 2894 5.04 %
Rwork0.2078 54478 -
obs0.2099 57372 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.97 Å2
Refinement stepCycle: LAST / Resolution: 1.87→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4849 0 33 426 5308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00645049
X-RAY DIFFRACTIONf_angle_d0.91146881
X-RAY DIFFRACTIONf_chiral_restr0.0583708
X-RAY DIFFRACTIONf_plane_restr0.008904
X-RAY DIFFRACTIONf_dihedral_angle_d13.8781801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90.34531480.31212515X-RAY DIFFRACTION99.7
1.9-1.930.35681290.29422525X-RAY DIFFRACTION99.48
1.93-1.970.35811130.27992523X-RAY DIFFRACTION99.58
1.97-2.010.36381110.27442564X-RAY DIFFRACTION99.66
2.01-2.050.34171180.25912568X-RAY DIFFRACTION99.67
2.05-2.090.31241370.25482523X-RAY DIFFRACTION99.77
2.09-2.140.31751410.24692529X-RAY DIFFRACTION99.78
2.14-2.190.28581240.23682559X-RAY DIFFRACTION99.96
2.19-2.250.34591330.2342554X-RAY DIFFRACTION99.74
2.25-2.320.28831530.23822520X-RAY DIFFRACTION99.63
2.32-2.390.25681320.23592568X-RAY DIFFRACTION99.85
2.39-2.480.28141360.23322561X-RAY DIFFRACTION99.93
2.48-2.580.25931510.2332575X-RAY DIFFRACTION99.85
2.58-2.70.25871290.23042631X-RAY DIFFRACTION100
2.7-2.840.28311480.22632551X-RAY DIFFRACTION99.89
2.84-3.020.28731460.22192617X-RAY DIFFRACTION100
3.02-3.250.25411360.22042612X-RAY DIFFRACTION99.93
3.25-3.580.26271600.19542634X-RAY DIFFRACTION99.96
3.58-4.090.22331520.16822662X-RAY DIFFRACTION100
4.09-5.150.15371330.14932737X-RAY DIFFRACTION99.97
5.16-46.70.18731640.18012950X-RAY DIFFRACTION99.81

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