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- PDB-9ivz: Apg mutant enzyme D448A of acarbose hydrolase from human gut flor... -

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Basic information

Entry
Database: PDB / ID: 9ivz
TitleApg mutant enzyme D448A of acarbose hydrolase from human gut flora K. grimontii TD1, complex with acarbose
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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
DepositionJul 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 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)69,7102
Polymers69,0651
Non-polymers6461
Water5,332296
1
A: Maltodextrin glucosidase
hetero molecules

A: Maltodextrin glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,4204
Polymers138,1292
Non-polymers1,2912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area4140 Å2
ΔGint-5 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.480, 75.480, 400.802
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

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Components

#1: Protein Maltodextrin glucosidase / Apg


Mass: 69064.633 Da / Num. of mol.: 1 / Mutation: D448A
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-(1-4)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 645.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
DescriptorTypeProgram
[][b-D-Galp]{[(4+1)][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.: 296 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M DL-malic acid

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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: 2.29→37.74 Å / Num. obs: 31827 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 32.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Net I/σ(I): 10.9
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3044 / CC1/2: 0.865 / % possible all: 100

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Processing

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

7vt9


Resolution: 2.29→37.74 Å / SU ML: 0.2622 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 1599 5.04 %
Rwork0.1862 30114 -
obs0.1885 31713 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.34 Å2
Refinement stepCycle: LAST / Resolution: 2.29→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4869 0 44 296 5209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00655065
X-RAY DIFFRACTIONf_angle_d0.99116898
X-RAY DIFFRACTIONf_chiral_restr0.0856711
X-RAY DIFFRACTIONf_plane_restr0.0082903
X-RAY DIFFRACTIONf_dihedral_angle_d14.47811813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.360.32331520.25342643X-RAY DIFFRACTION99.68
2.36-2.450.30571500.24362643X-RAY DIFFRACTION99.5
2.45-2.550.31881410.24352660X-RAY DIFFRACTION99.5
2.55-2.660.30051430.23382684X-RAY DIFFRACTION99.54
2.66-2.80.2981410.23572689X-RAY DIFFRACTION99.44
2.8-2.980.29781370.22382707X-RAY DIFFRACTION99.75
2.98-3.210.27761330.21442715X-RAY DIFFRACTION99.48
3.21-3.530.24941470.19622732X-RAY DIFFRACTION99.21
3.53-4.040.20351400.15472775X-RAY DIFFRACTION99.97
4.04-5.090.16461580.13342830X-RAY DIFFRACTION99.7
5.09-37.740.16911570.15893036X-RAY DIFFRACTION98.76

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