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- PDB-9sji: Crystal structure of SGBPdex (BT3088) with truncated residues 1-147 -

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Basic information

Entry
Database: PDB / ID: 9sji
TitleCrystal structure of SGBPdex (BT3088) with truncated residues 1-147
ComponentsBT3088 (SGBPdex)
KeywordsSUGAR BINDING PROTEIN / dextran / Bacteroides / SGBP / utilisome / glycan-binding / surface glycan binding protein / SGBPdex
Function / homologySusE outer membrane protein / SusE outer membrane protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / SusE outer membrane protein domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: BT3088 (SGBPdex)


Theoretical massNumber of molelcules
Total (without water)40,7991
Polymers40,7991
Non-polymers00
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.321, 37.549, 65.616
Angle α, β, γ (deg.)90, 100.345, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BT3088 (SGBPdex)


Mass: 40799.285 Da / Num. of mol.: 1 / Mutation: deleted residues 1-147
Source method: isolated from a genetically manipulated source
Details: N-terminal synthetic His6-tag. N-terminal truncation to remove the Ig-like NTD. All three putative carbohydrate binding modules (CBM) were included in the construct.
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3088
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A367
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MPD 1k 3350 35.5% w/v 200mM amino acid stock 100mM System 2 buffer (0.1M HEPES sodium salt and 0.1M MOPS at pH 7.5) pH 7.5

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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: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89842 Å / Relative weight: 1
ReflectionResolution: 1.7→36.48 Å / Num. obs: 39600 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.054 / Rrim(I) all: 0.103 / Χ2: 0.93 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9-36.486.40.03430.23060.9970.020.0390.3699.1
1.7-1.7372.0630.720690.7131.2642.4240.91100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
Aimlessdata scaling
xia2data scaling
Cootmodel building
PHENIXphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.477 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.605 / SU ML: 0.159 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.27 2011 5.081 %
Rwork0.1982 37564 -
all0.202 --
obs-39575 99.929 %
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: 43.417 Å2
Baniso -1Baniso -2Baniso -3
1--3.752 Å2-0 Å21.644 Å2
2--0.982 Å2-0 Å2
3---2.034 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 0 347 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122816
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162540
X-RAY DIFFRACTIONr_angle_refined_deg2.2141.8133826
X-RAY DIFFRACTIONr_angle_other_deg0.8991.7595888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7685349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.18357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47710460
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.57110128
X-RAY DIFFRACTIONr_chiral_restr0.1160.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023319
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02635
X-RAY DIFFRACTIONr_nbd_refined0.2080.2592
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22551
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21363
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21469
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0680.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1390.222
X-RAY DIFFRACTIONr_nbd_other0.1430.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.219
X-RAY DIFFRACTIONr_mcbond_it4.8764.0031399
X-RAY DIFFRACTIONr_mcbond_other4.8684.0031399
X-RAY DIFFRACTIONr_mcangle_it6.0297.1811747
X-RAY DIFFRACTIONr_mcangle_other6.0317.1831748
X-RAY DIFFRACTIONr_scbond_it6.2324.3911417
X-RAY DIFFRACTIONr_scbond_other6.234.3911417
X-RAY DIFFRACTIONr_scangle_it8.5557.8542079
X-RAY DIFFRACTIONr_scangle_other8.5537.8552080
X-RAY DIFFRACTIONr_lrange_it29.70547.7363344
X-RAY DIFFRACTIONr_lrange_other28.98846.5123276
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
1.7-1.7440.4381320.42527250.42628630.8390.8299.79040.414
1.744-1.7920.3941440.38927170.3928620.8380.85199.96510.374
1.792-1.8440.361580.34325610.34427220.8630.87499.88980.318
1.844-1.90.3491330.34925400.34926740.8730.88199.96260.327
1.9-1.9620.3691180.30824820.31126030.8910.90299.88480.288
1.962-2.0310.3071290.25223580.25524910.9270.94899.83940.232
2.031-2.1070.2841360.23822860.2424230.9380.95899.95870.218
2.107-2.1930.3051220.23422180.23723410.9270.9699.95730.213
2.193-2.290.2911100.19821140.20322250.9440.97399.95510.179
2.29-2.4020.2861050.20220270.20621330.9430.97299.95310.182
2.402-2.5310.3221010.19919700.20420710.9360.9741000.183
2.531-2.6840.296960.20418330.20819300.9470.97499.94820.189
2.684-2.8680.3940.20117350.20718290.9390.9731000.19
2.868-3.0960.279840.20416160.20817000.9470.9741000.196
3.096-3.3890.29720.20614950.2115670.9480.9741000.204
3.389-3.7850.271790.18313630.18714420.9610.9821000.184
3.785-4.3630.253650.14311950.14812610.9650.98899.92070.152
4.363-5.3240.147520.1210340.12210860.9880.9931000.131
5.324-7.450.211520.1398060.1448580.9790.9891000.145
7.45-36.4770.195290.1344890.1375180.9820.9881000.141

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