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- PDB-9vd8: Structure of a truncated loopA mutant from the human gut flora K.... -

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Basic information

Entry
Database: PDB / ID: 9vd8
TitleStructure of a truncated loopA mutant from the human gut flora K. grimontii Apg in complex with glucose
ComponentsApg-truncated loopA
KeywordsHYDROLASE / Complex
Function / homologyalpha-D-glucopyranose
Function and homology information
Biological speciesKlebsiella grimontii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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
DepositionJun 7, 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: Apg-truncated loopA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5852
Polymers67,4051
Non-polymers1801
Water4,125229
1
A: Apg-truncated loopA
hetero molecules

A: Apg-truncated loopA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1704
Polymers134,8102
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area5020 Å2
ΔGint-4 kcal/mol
Surface area42030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.870, 75.870, 401.959
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
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 Apg-truncated loopA


Mass: 67404.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella grimontii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES PH=7.5, 20% w/v Poly(acrylic acid sodium salt)5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→46.91 Å / Num. obs: 28627 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 40.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.6
Reflection shellResolution: 2.39→2.48 Å / Rmerge(I) obs: 0.992 / Num. unique obs: 2899 / CC1/2: 0.851

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→46.91 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 1414 4.96 %
Rwork0.1911 --
obs0.1934 28492 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 12 229 4913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074827
X-RAY DIFFRACTIONf_angle_d0.8736573
X-RAY DIFFRACTIONf_dihedral_angle_d14.3521733
X-RAY DIFFRACTIONf_chiral_restr0.185674
X-RAY DIFFRACTIONf_plane_restr0.008865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.480.32971250.24952611X-RAY DIFFRACTION100
2.48-2.570.29251240.24152647X-RAY DIFFRACTION100
2.57-2.690.3161360.24912640X-RAY DIFFRACTION100
2.69-2.830.29441510.23862630X-RAY DIFFRACTION100
2.83-3.010.28561370.22912668X-RAY DIFFRACTION100
3.01-3.240.28561340.21552678X-RAY DIFFRACTION100
3.24-3.570.26551400.20462702X-RAY DIFFRACTION100
3.57-4.090.18931550.16922726X-RAY DIFFRACTION100
4.09-5.150.1971480.14362780X-RAY DIFFRACTION100
5.15-46.910.20021640.17432996X-RAY DIFFRACTION100

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