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- PDB-9vdw: Structure of truncated loopA and loopB mutants from the human gut... -

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Basic information

Entry
Database: PDB / ID: 9vdw
TitleStructure of truncated loopA and loopB mutants from the human gut flora K. grimontii Apg
ComponentsAcarbose hydrolase
KeywordsHYDROLASE
Biological speciesKlebsiella grimontii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 9, 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

Downloads & links

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Assembly

Deposited unit
A: Acarbose hydrolase
B: Acarbose hydrolase
C: Acarbose hydrolase
D: Acarbose hydrolase


Theoretical massNumber of molelcules
Total (without water)248,3894
Polymers248,3894
Non-polymers00
Water8,755486
1
A: Acarbose hydrolase
B: Acarbose hydrolase


Theoretical massNumber of molelcules
Total (without water)124,1942
Polymers124,1942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Acarbose hydrolase
D: Acarbose hydrolase


Theoretical massNumber of molelcules
Total (without water)124,1942
Polymers124,1942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.210, 70.893, 130.330
Angle α, β, γ (deg.)87.637, 79.984, 89.929
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 16 or (resid 17...
d_2ens_1(chain "B" and (resid 2 through 16 or (resid 17...
d_3ens_1(chain "C" and (resid 2 through 16 or (resid 17...
d_4ens_1(chain "D" and (resid 2 through 33 or (resid 34...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUSERSERAA2 - 1362 - 136
d_12PHEPHEVALVALAA159 - 189159 - 189
d_13ARGARGSERSERAA202 - 385202 - 385
d_14ALAALAARGARGAA387 - 544387 - 544
d_21LEULEUALAALABB2 - 392 - 39
d_22ASPASPLEULEUBB42 - 27442 - 274
d_23ILEILESERSERBB293 - 385293 - 385
d_24ALAALAARGARGBB387 - 544387 - 544
d_31LEULEUALAALACC2 - 392 - 39
d_32ASPASPSERSERCC42 - 13642 - 136
d_33PHEPHELEULEUCC159 - 274159 - 274
d_34ILEILESERSERCC293 - 385293 - 385
d_35ALAALAASPASPCC387 - 427387 - 427
d_36LYSLYSARGARGCC436 - 544436 - 544
d_41LEULEUALAALADD2 - 392 - 39
d_42ASPASPVALVALDD42 - 18942 - 189
d_43ARGARGLEULEUDD202 - 274202 - 274
d_44ILEILESERSERDD293 - 385293 - 385
d_45ALAALAARGARGDD387 - 544387 - 544

NCS oper:
IDCodeMatrixVector
1given(0.787448584284, 0.00645842525834, -0.616346506319), (0.0110609931521, -0.999932149967, 0.00365375048185), (-0.616281089714, -0.00969454512999, -0.787466592469)8.63490641992, -30.5809381338, 24.9650642143
2given(0.785791515786, 0.00813777485928, -0.618437927636), (-0.0138411199046, 0.999894396259, -0.00442941641801), (0.618336572683, 0.0120404713511, 0.78582116918)0.368808797299, -2.67034361836, 68.9720830067
3given(0.999997712034, -0.000320168537741, 0.00211504560736), (-0.000320977627035, -0.999999875444, 0.000382211515491), (0.00211492297181, -0.000382889523325, -0.999997690246)-8.4071795544, -33.2640588964, 93.8413057901

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Components

#1: Protein
Acarbose hydrolase


Mass: 62097.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella grimontii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Citric acid pH=5, 5% w/v PEG 6000

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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: Jun 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.38→128.23 Å / Num. obs: 85164 / % possible obs: 96.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.95 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.4
Reflection shellResolution: 2.38→2.42 Å / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4484 / CC1/2: 0.636

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→35.42 Å / SU ML: 0.3239 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 26.5564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 4294 5.04 %
Rwork0.1988 80822 -
obs0.2012 85116 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.25 Å2
Refinement stepCycle: LAST / Resolution: 2.38→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14816 0 0 486 15302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815259
X-RAY DIFFRACTIONf_angle_d0.988220751
X-RAY DIFFRACTIONf_chiral_restr0.0592186
X-RAY DIFFRACTIONf_plane_restr0.00922692
X-RAY DIFFRACTIONf_dihedral_angle_d13.60495483
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.554902188756
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.575065188675
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.366064147521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.410.29481560.24422651X-RAY DIFFRACTION95.9
2.41-2.440.33121290.25012654X-RAY DIFFRACTION95.67
2.44-2.470.30821420.23582695X-RAY DIFFRACTION96.14
2.47-2.50.27751550.23322686X-RAY DIFFRACTION96.83
2.5-2.530.32991250.24262694X-RAY DIFFRACTION97.11
2.53-2.560.30671370.24212693X-RAY DIFFRACTION96.82
2.56-2.60.35641290.25092768X-RAY DIFFRACTION97.21
2.6-2.640.26941450.23822662X-RAY DIFFRACTION97.33
2.64-2.680.28141470.23922665X-RAY DIFFRACTION96.83
2.68-2.720.321450.23362763X-RAY DIFFRACTION97.65
2.72-2.770.31791210.23042715X-RAY DIFFRACTION97.16
2.77-2.820.28051630.22382678X-RAY DIFFRACTION96.67
2.82-2.880.27421410.22152656X-RAY DIFFRACTION97.25
2.88-2.930.28021320.22352741X-RAY DIFFRACTION97
2.93-30.2881410.22522666X-RAY DIFFRACTION96.96
3-3.070.31451180.22112749X-RAY DIFFRACTION97.32
3.07-3.140.28461180.22092758X-RAY DIFFRACTION97.76
3.14-3.230.2931640.21992688X-RAY DIFFRACTION97.37
3.23-3.320.2571620.21692675X-RAY DIFFRACTION97.56
3.32-3.430.28041450.20842723X-RAY DIFFRACTION97.06
3.43-3.550.25011700.20242647X-RAY DIFFRACTION96.8
3.55-3.70.26611540.1942686X-RAY DIFFRACTION96.76
3.7-3.860.20241300.18992679X-RAY DIFFRACTION96.1
3.86-4.070.2261320.17262672X-RAY DIFFRACTION95.73
4.07-4.320.20211450.16312679X-RAY DIFFRACTION96.78
4.32-4.660.18831820.15282673X-RAY DIFFRACTION97.31
4.66-5.120.20051230.15822731X-RAY DIFFRACTION97.04
5.12-5.860.21270.17032711X-RAY DIFFRACTION96.89
5.86-7.370.24181770.21132660X-RAY DIFFRACTION97.26
7.38-35.420.19811390.182704X-RAY DIFFRACTION96.93

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