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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 Bacteroides thetaiotaomicron
Authors: Feasey, M. / Silale, A. / Basle, A. / van den Berg, B.
History
DepositionAug 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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