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- PDB-9v0i: Apg mutant enzyme D448N of the human gut flora K. grimontii TD1 a... -

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Basic information

Entry
Database: PDB / ID: 9v0i
TitleApg mutant enzyme D448N of the human gut flora K. grimontii TD1 acarbose hydrolase
ComponentsMaltodextrin glucosidase
KeywordsHYDROLASE
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: 2.3 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
DepositionMay 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltodextrin glucosidase


Theoretical massNumber of molelcules
Total (without water)69,1081
Polymers69,1081
Non-polymers00
Water3,261181
1
A: Maltodextrin glucosidase

A: Maltodextrin glucosidase


Theoretical massNumber of molelcules
Total (without water)138,2152
Polymers138,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area4240 Å2
ΔGint-7 kcal/mol
Surface area43320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.499, 75.499, 401.388
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-752-

HOH

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Components

#1: Protein Maltodextrin glucosidase


Mass: 69107.656 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M BICINE 1.6M 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: Apr 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.3→37.75 Å / Num. obs: 31203 / % possible obs: 99.3 % / Redundancy: 10.1 % / Biso Wilson estimate: 36.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Net I/σ(I): 17.2
Reflection shellResolution: 2.3→2.3 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3015 / CC1/2: 0.892 / % 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 / Resolution: 2.3→37.75 Å / SU ML: 0.3333 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2658 1544 4.96 %
Rwork0.2173 29611 -
obs0.2197 31155 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4795 0 0 181 4976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744941
X-RAY DIFFRACTIONf_angle_d0.8976718
X-RAY DIFFRACTIONf_chiral_restr0.0582680
X-RAY DIFFRACTIONf_plane_restr0.0084885
X-RAY DIFFRACTIONf_dihedral_angle_d14.66761784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.39081360.28332649X-RAY DIFFRACTION99.82
2.37-2.460.33271010.26722644X-RAY DIFFRACTION99.17
2.46-2.560.35571520.27122631X-RAY DIFFRACTION99.71
2.56-2.670.29351380.26922664X-RAY DIFFRACTION99.75
2.67-2.810.32321380.25922658X-RAY DIFFRACTION99.43
2.81-2.990.30581390.25462668X-RAY DIFFRACTION99.33
2.99-3.220.32661470.25642646X-RAY DIFFRACTION98.41
3.22-3.550.29131350.232708X-RAY DIFFRACTION99.44
3.55-4.060.21421300.19152729X-RAY DIFFRACTION99
4.06-5.110.21171630.16592722X-RAY DIFFRACTION97.27
5.11-37.750.23231650.18892892X-RAY DIFFRACTION95.53

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