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- PDB-9sjk: Crystal structure of apo SusDdex (BT3089) -

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Basic information

Entry
Database: PDB / ID: 9sjk
TitleCrystal structure of apo SusDdex (BT3089)
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / BT3089 / SusDdex / SusD / dextran / Bacteroides / glycan-binding
Function / homologySusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / SusD homolog
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SusD homolog
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,97316
Polymers107,6282
Non-polymers1,34514
Water22,3391240
1
A: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2946
Polymers53,8141
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,67910
Polymers53,8141
Non-polymers8659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.5, 119.5, 176.98
Angle α, β, γ (deg.)90, 90, 90
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: HIS / End label comp-ID: HIS

Dom-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA36 - 50310 - 477
2BB36 - 50110 - 475

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

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Components

#1: Protein SusD homolog


Mass: 53814.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3089
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A366
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1240 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Citric acid pH 5 0.8M ammonium sulphate Cryoprotected in 3.5M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.65→53.44 Å / Num. obs: 153600 / % possible obs: 100 % / Redundancy: 50.9 % / CC1/2: 1 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.029 / Rrim(I) all: 0.15 / Χ2: 1.03 / Net I/σ(I): 19.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.04-53.4448.50.04875.4111110.0090.0490.7999.6
1.65-1.68514.128175180.8330.8164.2090.81100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Cootmodel building
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→53.44 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.784 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.084 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2057 7727 5.033 %
Rwork0.1804 145786 -
all0.182 --
obs-153513 99.993 %
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: 29.795 Å2
Baniso -1Baniso -2Baniso -3
1-0.858 Å2-0 Å2-0 Å2
2--0.858 Å20 Å2
3----1.717 Å2
Refinement stepCycle: LAST / Resolution: 1.65→53.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7394 0 70 1240 8704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0127618
X-RAY DIFFRACTIONr_angle_refined_deg2.0771.8110352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.503548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.336101226
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.66410386
X-RAY DIFFRACTIONr_chiral_restr0.1390.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025958
X-RAY DIFFRACTIONr_nbd_refined0.2110.23834
X-RAY DIFFRACTIONr_nbtor_refined0.3170.25328
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2900
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.263
X-RAY DIFFRACTIONr_mcbond_it2.1662.6113732
X-RAY DIFFRACTIONr_mcangle_it2.7324.6824658
X-RAY DIFFRACTIONr_scbond_it3.9492.933886
X-RAY DIFFRACTIONr_scangle_it5.5255.2425694
X-RAY DIFFRACTIONr_lrange_it8.38830.50312647
X-RAY DIFFRACTIONr_ncsr_local_group_10.0570.0516129
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.05730.05009
12BX-RAY DIFFRACTIONLocal ncs0.05730.05009
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
1.65-1.6930.3894910.356107250.358112160.9350.951000.336
1.693-1.7390.325570.281103780.283109350.9530.9621000.252
1.739-1.790.2865330.238100940.24106280.9580.9799.99060.206
1.79-1.8450.2685230.21398210.216103440.9610.9741000.182
1.845-1.9050.2265200.20294970.203100170.970.9761000.172
1.905-1.9720.2315020.18891930.1996950.9670.9781000.163
1.972-2.0460.2194660.17689150.17893810.970.9821000.157
2.046-2.1290.2084590.17185970.17390560.9740.9841000.155
2.129-2.2240.1934640.16982330.1786970.9770.9841000.151
2.224-2.3320.1964280.16378700.16582980.9770.9841000.148
2.332-2.4580.2123630.1775500.17279140.9730.98399.98740.155
2.458-2.6070.2143670.1871710.18275380.9710.981000.166
2.607-2.7870.2293630.1966940.19270570.970.9781000.178
2.787-3.0090.2213640.19562300.19665940.9680.9771000.188
3.009-3.2950.223110.20157980.20261090.9720.9771000.199
3.295-3.6830.1842720.16152850.16255570.9810.9861000.165
3.683-4.2490.1482660.12746660.12849320.9880.9911000.139
4.249-5.1960.1432170.12840060.12942230.990.9911000.145
5.196-7.3130.2361750.21531500.21633250.9730.9771000.236
7.313-53.440.221860.23719140.23620000.9710.9641000.289

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