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- PDB-9sjf: Crystal structure of GHdex dextranase (BT3087), E360A catalytic m... -

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Basic information

Entry
Database: PDB / ID: 9sjf
TitleCrystal structure of GHdex dextranase (BT3087), E360A catalytic mutant with bound IMO3
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: 2.2 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)134,19742
Polymers129,9012
Non-polymers4,29640
Water8,395466
1
A: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,96719
Polymers64,9501
Non-polymers2,01618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,23023
Polymers64,9501
Non-polymers2,27922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.224, 92.224, 328.033
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-991-

HOH

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: 3 - 570

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: 64950.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Co-crystallisation where the protein was pre-incubated with 5mM dextran 1.5 before being dispensed into trays Condition: 0.5M Lithium chloride 1.6M Ammonium sulphate

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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: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89842 Å / Relative weight: 1
ReflectionResolution: 2.2→47.03 Å / Num. obs: 73184 / % possible obs: 100 % / Redundancy: 24.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.319 / Rpim(I) all: 0.09 / Rrim(I) all: 0.332 / Χ2: 0.97 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
10.78-47.0322.60.09219.97690.9990.0250.0950.6199.1
2.2-2.2513.72.2251.144530.5050.8712.3971.02100

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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
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.294 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.701 / SU ML: 0.182 / Cross valid method: FREE R-VALUE / ESU R: 0.254 / ESU R Free: 0.219 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2617 3603 4.934 %
Rwork0.2017 69424 -
all0.205 --
obs-73027 99.947 %
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: 38.107 Å2
Baniso -1Baniso -2Baniso -3
1-1.137 Å2-0 Å2-0 Å2
2--1.137 Å2-0 Å2
3----2.274 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9000 0 234 466 9700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129436
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.81612850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2751134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.093532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.176101480
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.69610456
X-RAY DIFFRACTIONr_chiral_restr0.1240.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027294
X-RAY DIFFRACTIONr_nbd_refined0.2130.24337
X-RAY DIFFRACTIONr_nbtor_refined0.3120.26335
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2532
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2550.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.25
X-RAY DIFFRACTIONr_mcbond_it3.6583.5584542
X-RAY DIFFRACTIONr_mcangle_it4.9256.375674
X-RAY DIFFRACTIONr_scbond_it6.0043.9664894
X-RAY DIFFRACTIONr_scangle_it8.0747.0757176
X-RAY DIFFRACTIONr_lrange_it11.00938.19914297
X-RAY DIFFRACTIONr_ncsr_local_group_10.0670.0519276
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.06740.05009
12BX-RAY DIFFRACTIONLocal ncs0.06740.05009
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
2.2-2.2570.372470.32650420.32852890.90.9111000.324
2.257-2.3190.3152750.29648970.29751720.9280.9331000.288
2.319-2.3860.3242490.27147480.27449980.9310.94899.980.258
2.386-2.4590.322320.26146760.26449080.9310.9521000.243
2.459-2.5390.3732510.25144920.25847480.9140.95899.89470.23
2.539-2.6280.3452320.24543610.2545960.9360.96299.93470.221
2.628-2.7270.2912420.2342060.23344520.9480.96599.91010.205
2.727-2.8380.2922050.23140660.23442730.9480.96499.95320.205
2.838-2.9640.3092090.2339190.23441300.9430.96599.95160.206
2.964-3.1080.311760.22437550.22839330.9390.96799.94910.203
3.108-3.2750.2691900.2235980.22337880.9580.971000.201
3.275-3.4730.2411510.18233880.18535410.9620.98199.94350.168
3.473-3.7110.2131540.16732360.16933910.9730.98499.97050.155
3.711-4.0060.1951370.14730230.14931600.980.9881000.135
4.006-4.3850.191490.12927720.13229230.980.9999.93160.12
4.385-4.8970.1841330.14125250.14326580.980.9881000.131
4.897-5.6440.2241280.1722440.17323720.970.9831000.159
5.644-6.8870.2991170.20119390.20620560.9570.9771000.187
6.887-9.6340.222820.18915500.19116320.9670.9811000.179
9.634-46.2940.277440.2459870.24610340.9450.96499.70990.235

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