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- PDB-9hfj: Crystal structure of the NTE domain of SusCdex (BT3090) dextran t... -

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Basic information

Entry
Database: PDB / ID: 9hfj
TitleCrystal structure of the NTE domain of SusCdex (BT3090) dextran transporter
ComponentsSusC homolog
KeywordsTRANSPORT PROTEIN / NTE / TBDT / SusC / TonB / Bacteroides
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / THIOCYANATE ION / SusC homolog
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFeasey, M. / Basle, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the NTE domain of SusCdex (BT3090) dextran transporter
Authors: Feasey, M. / Basle, A. / van den Berg, B.
History
DepositionNov 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SusC homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,65810
Polymers8,9871
Non-polymers6719
Water1,53185
1
A: SusC homolog
hetero molecules

A: SusC homolog
hetero molecules

A: SusC homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,97530
Polymers26,9613
Non-polymers2,01427
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area4240 Å2
ΔGint-67 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.084, 62.084, 53.202
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21A-381-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SusC homolog / BT3090 (SusCdex) NTE


Mass: 8987.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Includes natural BT3090 residues 30-104.
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3090
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A365

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Non-polymers , 6 types, 94 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.89844 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89844 Å / Relative weight: 1
ReflectionResolution: 1.4→23.99 Å / Num. obs: 15041 / % possible obs: 99.7 % / Redundancy: 9.8 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.022 / Rrim(I) all: 0.051 / Χ2: 0.91 / Net I/σ(I): 21.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
7.54-23.9911.10.02491.3970.9990.0110.0271.1497.6
1.4-1.425.20.6321.87680.7120.4510.7820.6896.7

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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
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→23.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.169 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.066 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2064 773 5.14 %
Rwork0.1749 14265 -
all0.176 --
obs-15038 99.735 %
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: 22.406 Å2
Baniso -1Baniso -2Baniso -3
1-0.218 Å20.109 Å2-0 Å2
2--0.218 Å20 Å2
3----0.707 Å2
Refinement stepCycle: LAST / Resolution: 1.4→23.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 0 38 85 713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.012640
X-RAY DIFFRACTIONr_angle_refined_deg2.1951.788854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74710105
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.4781023
X-RAY DIFFRACTIONr_chiral_restr0.1080.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02446
X-RAY DIFFRACTIONr_nbd_refined0.210.2242
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2425
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.255
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3620.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.221
X-RAY DIFFRACTIONr_mcbond_it1.711.722330
X-RAY DIFFRACTIONr_mcangle_it2.3372.981408
X-RAY DIFFRACTIONr_scbond_it3.6022.353310
X-RAY DIFFRACTIONr_scangle_it4.9283.965445
X-RAY DIFFRACTIONr_lrange_it8.8831.568965
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
1.4-1.4360.289690.26310310.26511360.950.95896.8310.251
1.436-1.4760.277460.24510340.24610810.9550.96699.90750.229
1.476-1.5180.296470.21710000.22110470.9410.9731000.196
1.518-1.5650.24450.1959550.19710000.9670.9771000.171
1.565-1.6160.211580.1949520.19510100.9740.9771000.173
1.616-1.6720.203550.1869140.1879690.9720.9791000.167
1.672-1.7350.255650.1728660.1779310.9620.9821000.156
1.735-1.8060.273440.1658390.178830.9640.9831000.149
1.806-1.8850.177470.1668060.1678530.9780.9831000.153
1.885-1.9770.194300.1597750.168050.9790.9861000.15
1.977-2.0830.205400.1617490.1647890.9760.9871000.154
2.083-2.2080.193540.1756830.1767370.9810.9841000.168
2.208-2.3590.21320.1646570.1666890.9780.9841000.159
2.359-2.5460.201410.1676000.1696410.9730.9821000.164
2.546-2.7860.259240.1815600.1845840.960.9811000.176
2.786-3.110.209170.1755310.1765480.980.9811000.172
3.11-3.5810.152220.1714550.174770.9850.9821000.171
3.581-4.3610.184270.153740.1524010.9760.9851000.153
4.361-6.0680.18680.1662980.1663060.9820.9821000.169
6.068-23.990.39620.2151860.2171880.9970.9751000.216

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