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- PDB-9sjg: Crystal structure of apo GHdex dextranase (BT3087), wild type -

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Basic information

Entry
Database: PDB / ID: 9sjg
TitleCrystal structure of apo GHdex dextranase (BT3087), wild type
ComponentsCycloisomaltooligosaccharide glucanotransferase
KeywordsSUGAR BINDING PROTEIN / dextran / dextranase / Bacteroides / GH / glycoside hydrolase / enzyme / utilisome / GH66
Function / homologyGlycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Cycloisomaltooligosaccharide glucanotransferase
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFeasey, M. / Basle, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: J Struct Biol X / Year: 2026
Title: Structural and functional characterisation of the dextran utilisome from .
Authors: Matthew Feasey / Augustinas Silale / Arnaud Baslé / Bert van den Berg /
Abstract: () is a model Bacteroidota of the healthy human gut microbiota and a specialist in glycan utilisation. Like other , has many highly regulated polysaccharide utilisation loci (PUL) that encode outer ... () is a model Bacteroidota of the healthy human gut microbiota and a specialist in glycan utilisation. Like other , has many highly regulated polysaccharide utilisation loci (PUL) that encode outer membrane (OM) TonB-dependent transporters (SusC), closely associated "lid" lipoproteins (SusD), and additional surface-exposed lipoproteins (SLPs) that bind and partially degrade specific glycans derived from host cells, diet, or other microbiota members. The canonical starch PUL products are thought to form a dynamic complex in the presence of starch. However, other PULs form stable complexes in the absence of substrate (recently named "utilisomes"), with additional surface lipoproteins tightly associated with the core SusCD complex. In this study, we characterised the dextran utilisome, with a SusCD core and an associated glycoside hydrolase (GH) and surface glycan binding protein (SBGP). Via X-ray crystallography we solved high-resolution structures of SBGP in isolation and SusD and GH bound to dextran oligosaccharides. We used isothermal titration calorimetry (ITC) to quantify ligand binding of wild type and mutant SLPs. We further used single particle cryo-EM of the catalytically inactive dextran utilisome to visualise open and closed states of the complex. Three occupied dextran binding sites were observed across SusC, SusD and GH, with substrate observed in both open and closed states of SusD. 3D variability analysis showed a minority of particles in the process of SusD lid closure. Together our work defines commonalities and differences across utilisomes dedicated to the import of simple glycans.
History
DepositionAug 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cycloisomaltooligosaccharide glucanotransferase
B: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,58527
Polymers130,1312
Non-polymers2,45425
Water25,5451418
1
A: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,43715
Polymers65,0661
Non-polymers1,37114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,14812
Polymers65,0661
Non-polymers1,08311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.698, 93.698, 331.612
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 27 - 594 / Label seq-ID: 4 - 571

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Cycloisomaltooligosaccharide glucanotransferase


Mass: 65065.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal truncation (1-25) to express the lipoprotein as a soluble protein C-terminal "LEHHHHHH" from pET28b vector for purifiation
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3087
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A368
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1418 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES 0.8-3.2M ammonium sulphate / PH range: 6-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.89842 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89842 Å / Relative weight: 1
ReflectionResolution: 1.8→55.27 Å / Num. obs: 137723 / % possible obs: 100 % / Redundancy: 25.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.046 / Rrim(I) all: 0.167 / Χ2: 0.84 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.86-55.2723.10.03541.4103510.0090.0360.3499.5
1.8-1.8327.32.2391.667040.810.6182.3230.63100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Aimlessdata scaling
DIALSdata collection
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→54.133 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.096 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.119 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2291 6909 5.027 %
Rwork0.1982 130527 -
all0.2 --
obs-137436 99.9 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.862 Å2
Baniso -1Baniso -2Baniso -3
1-0.952 Å2-0 Å2-0 Å2
2--0.952 Å2-0 Å2
3----1.905 Å2
Refinement stepCycle: LAST / Resolution: 1.8→54.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9008 0 131 1418 10557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0129361
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.80912733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01551136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.941532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.967101487
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.32510458
X-RAY DIFFRACTIONr_chiral_restr0.1320.21364
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027310
X-RAY DIFFRACTIONr_nbd_refined0.2320.24424
X-RAY DIFFRACTIONr_nbtor_refined0.3120.26296
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.21027
X-RAY DIFFRACTIONr_metal_ion_refined0.5890.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2840.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.245
X-RAY DIFFRACTIONr_mcbond_it2.6272.7064547
X-RAY DIFFRACTIONr_mcangle_it3.294.8475682
X-RAY DIFFRACTIONr_scbond_it4.3033.0634814
X-RAY DIFFRACTIONr_scangle_it6.0745.467051
X-RAY DIFFRACTIONr_lrange_it23.01835.89614896
X-RAY DIFFRACTIONr_ncsr_local_group_10.0660.0519181
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.066480.05009
12BX-RAY DIFFRACTIONLocal ncs0.066480.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3495200.28694460.28999890.9210.94499.76970.264
1.847-1.8970.3074980.27492540.27697720.9390.95199.79530.248
1.897-1.9520.3014450.24390870.24595620.9450.96199.68630.214
1.952-2.0120.2674910.2387090.23292070.9540.96599.9240.202
2.012-2.0780.2424430.21785080.21889630.9590.96999.86610.19
2.078-2.1510.2574150.2182300.21386540.9590.97299.8960.185
2.151-2.2320.2414300.19979980.20184310.9630.97599.96440.175
2.232-2.3230.2823840.20276840.20680730.9510.97499.93810.177
2.323-2.4260.2573870.20173680.20477570.960.97599.97420.176
2.426-2.5440.2713950.20570570.20874560.9570.97499.94640.18
2.544-2.6810.2523820.2167130.21370990.9590.97299.94370.187
2.681-2.8440.2483230.21464150.21567410.9630.97299.95550.192
2.844-3.0390.2742800.23160480.23363290.9480.96899.98420.214
3.039-3.2820.2433080.21556170.21759250.9610.9741000.203
3.282-3.5940.1912740.18552230.18554980.9790.98399.98180.179
3.594-4.0160.1762530.15247320.15349870.9820.98799.95990.149
4.016-4.6330.1522330.12442120.12644450.9870.9911000.124
4.633-5.6640.1711890.15536160.15638050.9840.9881000.155
5.664-7.9670.2431630.23228680.23330320.9710.97499.9670.228
7.967-54.1330.232960.24317420.24218390.970.96399.94560.25

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