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

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Basic information

Entry
Database: PDB / ID: 9vdg
TitleStructure of a truncated loopB mutant from the human gut flora K. grimontii Apg
ComponentsAPG-truncated loopB
KeywordsHYDROLASE
Biological speciesKlebsiella grimontii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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 8, 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 loopB
B: APG-truncated loopB
C: APG-truncated loopB
D: APG-truncated loopB


Theoretical massNumber of molelcules
Total (without water)255,3804
Polymers255,3804
Non-polymers00
Water5,621312
1
A: APG-truncated loopB
B: APG-truncated loopB


Theoretical massNumber of molelcules
Total (without water)127,6902
Polymers127,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: APG-truncated loopB
D: APG-truncated loopB


Theoretical massNumber of molelcules
Total (without water)127,6902
Polymers127,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.364, 70.890, 130.304
Angle α, β, γ (deg.)92.540, 100.137, 90.078
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 18 or (resid 19...
d_2ens_1(chain "B" and (resid 2 through 15 or (resid 16...
d_3ens_1(chain "C" and (resid 2 through 13 or (resid 14...
d_4ens_1(chain "D" and (resid 2 through 17 or (resid 18...

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_11LEULEUPHEPHEAA2 - 2032 - 203
d_12ARGARGASNASNAA218 - 444218 - 444
d_13LYSLYSARGARGAA451 - 559451 - 559
d_21LEULEUPHEPHEBB2 - 2032 - 203
d_22ARGARGARGARGBB218 - 559218 - 559
d_31LEULEUGLUGLUCC2 - 402 - 40
d_32ASNASNSERSERCC43 - 13643 - 136
d_33TYRTYRARGARGCC175 - 559175 - 559
d_41LEULEUPHEPHEDD2 - 2032 - 203
d_42ARGARGASNASNDD218 - 444218 - 444
d_43LYSLYSARGARGDD451 - 559451 - 559

NCS oper:
IDCodeMatrixVector
1given(0.787853368037, 0.00448958153181, 0.615846502086), (0.00776024749288, -0.999966409607, -0.00263784302348), (0.615813972749, 0.00685735478421, -0.787861743996)-9.34653909781, 25.3166853771, 26.9208187904
2given(0.787238893249, 0.00558169721069, 0.616622874708), (-0.0106759728567, 0.999932528101, 0.00457852046835), (-0.616555714076, -0.0101874384594, 0.787245366793)-1.08378590907, 2.16176026002, 68.6605490922
3given(0.99999747518, 0.0022384085126, -0.000197891002498), (0.00223827956769, -0.999997284167, -0.000649433372942), (-0.00019934416225, 0.000648988797852, -0.999999769538)8.22192966819, 27.5194551294, 95.4909479368

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Components

#1: Protein
APG-truncated loopB


Mass: 63844.957 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.: 312 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M Citric acid pH 5.0 5% w/v Polyethylene glycol 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: Apr 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.67→48.62 Å / Num. obs: 56672 / % possible obs: 90.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 33.17 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.3
Reflection shellResolution: 2.67→2.75 Å / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4734 / CC1/2: 0.877

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→48.62 Å / SU ML: 0.3676 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 27.5922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.269 2786 4.92 %
Rwork0.2392 53864 -
obs0.2407 56650 90.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.76 Å2
Refinement stepCycle: LAST / Resolution: 2.67→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14537 0 0 312 14849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005814944
X-RAY DIFFRACTIONf_angle_d0.959820348
X-RAY DIFFRACTIONf_chiral_restr0.05472161
X-RAY DIFFRACTIONf_plane_restr0.00742648
X-RAY DIFFRACTIONf_dihedral_angle_d14.0575304
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.487004429123
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.522092488063
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.41316874733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.720.33821530.28682760X-RAY DIFFRACTION92.24
2.72-2.770.33161520.28152721X-RAY DIFFRACTION92.44
2.77-2.820.29211580.2732729X-RAY DIFFRACTION92.47
2.82-2.880.30461350.26312706X-RAY DIFFRACTION91.82
2.88-2.940.30261310.26982732X-RAY DIFFRACTION91.62
2.94-3.010.29471110.27672655X-RAY DIFFRACTION90.16
3.01-3.080.33371390.26822684X-RAY DIFFRACTION88.75
3.08-3.170.33371190.26432474X-RAY DIFFRACTION84
3.17-3.260.31461200.25742626X-RAY DIFFRACTION86.76
3.26-3.360.25581430.25432794X-RAY DIFFRACTION94.83
3.36-3.480.30551350.24292764X-RAY DIFFRACTION93.97
3.48-3.620.25941380.23612826X-RAY DIFFRACTION94.18
3.62-3.790.27061450.2252756X-RAY DIFFRACTION93.88
3.79-3.990.2361270.21062730X-RAY DIFFRACTION91.89
3.99-4.240.19271240.19862703X-RAY DIFFRACTION91.05
4.24-4.560.20861330.19842595X-RAY DIFFRACTION87.41
4.56-5.020.21461420.19972565X-RAY DIFFRACTION86.51
5.02-5.750.25332020.21712772X-RAY DIFFRACTION95.32
5.75-7.240.31151310.26652789X-RAY DIFFRACTION93.5
7.24-48.620.29141480.27132483X-RAY DIFFRACTION84.6

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