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- PDB-9ixh: Apg mutant enzyme D448A of the human gut flora K. grimontii TD1 a... -

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Basic information

Entry
Database: PDB / ID: 9ixh
TitleApg mutant enzyme D448A 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: 2.43 Å
AuthorsZhou, J.H. / Huang, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Apg mutant enzyme D448A of the human gut flora K. grimontii TD1 acarbose hydrolase
Authors: Zhou, J.H. / Huang, J.Y.
History
DepositionJul 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 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)69,0651
Polymers69,0651
Non-polymers00
Water2,882160
1
A: Maltodextrin glucosidase

A: Maltodextrin glucosidase


Theoretical massNumber of molelcules
Total (without water)138,1292
Polymers138,1292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area4130 Å2
ΔGint-4 kcal/mol
Surface area43700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.797, 75.797, 405.549
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-860-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.7 M Sodium citrate tribasic dihydrate 0.1M Tris, PH=8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98655 Å / Relative weight: 1
ReflectionResolution: 2.43→20 Å / Num. obs: 27421 / % possible obs: 99.8 % / Redundancy: 8.2 % / Biso Wilson estimate: 45.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Net I/σ(I): 13.6
Reflection shellResolution: 2.43→2.43 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3026 / CC1/2: 0.791 / % possible all: 100

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Processing

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

7vt9


Resolution: 2.43→20 Å / SU ML: 0.2882 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2435 1368 5.01 %
Rwork0.2166 25927 -
obs0.218 27295 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.04 Å2
Refinement stepCycle: LAST / Resolution: 2.43→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4819 0 0 160 4979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244967
X-RAY DIFFRACTIONf_angle_d0.56576759
X-RAY DIFFRACTIONf_chiral_restr0.0436686
X-RAY DIFFRACTIONf_plane_restr0.0056892
X-RAY DIFFRACTIONf_dihedral_angle_d13.60671788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.520.33171240.30282525X-RAY DIFFRACTION100
2.52-2.620.3111400.30192518X-RAY DIFFRACTION99.89
2.62-2.740.35651380.29222516X-RAY DIFFRACTION99.96
2.74-2.880.28821470.27662501X-RAY DIFFRACTION99.96
2.88-3.060.31081250.27952568X-RAY DIFFRACTION99.93
3.06-3.30.31711140.25542601X-RAY DIFFRACTION99.89
3.3-3.620.24761450.22492557X-RAY DIFFRACTION100
3.63-4.150.22561260.18962626X-RAY DIFFRACTION100
4.15-5.210.16521500.16042649X-RAY DIFFRACTION100
5.21-200.22761590.18492866X-RAY DIFFRACTION99.93

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