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- PDB-7bll: Structure of SusD homologue BT3013 from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 7bll
TitleStructure of SusD homologue BT3013 from Bacteroides thetaiotaomicron
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / Bacteroides thetaiotaomicron / surface glycan-binding protein (SusD homologue) / gut microbiome / mucins
Function / homologySusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Tetratricopeptide-like helical domain superfamily / membrane / DI(HYDROXYETHYL)ETHER / SusD homolog
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsCosta, R.L.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)PTDC/BIA-MIB/31730/2017 Portugal
CitationJournal: To Be Published
Title: Structural basis for mucin-type O-glycan recognition by proteins of a Bacteroides thetaiotaomicron polysaccharide utilization loci
Authors: Costa, R.L. / Correia, V.G.
History
DepositionJan 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5893
Polymers73,4211
Non-polymers1682
Water10,269570
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint3 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.530, 65.830, 87.020
Angle α, β, γ (deg.)90.000, 95.830, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1227-

HOH

21A-1246-

HOH

31A-1330-

HOH

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Components

#1: Protein SusD homolog / Surface glycan-binding protein (SusD homologue) from Bacteroides thetaiotaomicron


Mass: 73420.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3013
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A3E1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 14mg/ml 30% w/v PEG 4000, 0.1 M sodium citrate pH 5.5 and 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.76→86.57 Å / Num. obs: 372154 / % possible obs: 99.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 17.66 Å2 / CC1/2: 0.994 / Net I/σ(I): 15.5
Reflection shellResolution: 1.76→1.8 Å / Num. unique obs: 19950 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→56.97 Å / SU ML: 0.2002 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.8474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2001 6359 5.12 %
Rwork0.1626 117871 -
obs0.1645 124230 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.61 Å2
Refinement stepCycle: LAST / Resolution: 1.76→56.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4825 0 11 570 5406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01225010
X-RAY DIFFRACTIONf_angle_d1.11926820
X-RAY DIFFRACTIONf_chiral_restr0.0593720
X-RAY DIFFRACTIONf_plane_restr0.0094892
X-RAY DIFFRACTIONf_dihedral_angle_d6.5136703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.28022240.22953990X-RAY DIFFRACTION99.29
1.78-1.80.32251720.21713904X-RAY DIFFRACTION99.51
1.8-1.820.29562090.23353934X-RAY DIFFRACTION99.4
1.83-1.850.31382110.23573926X-RAY DIFFRACTION99.02
1.85-1.870.28542270.23323928X-RAY DIFFRACTION99.4
1.87-1.90.26651990.21753948X-RAY DIFFRACTION99.26
1.9-1.930.2382290.22073845X-RAY DIFFRACTION99.22
1.93-1.950.27272210.22033947X-RAY DIFFRACTION99.29
1.95-1.980.27112600.24583832X-RAY DIFFRACTION99.15
1.98-2.020.24452310.22713908X-RAY DIFFRACTION99.33
2.02-2.050.22122010.19934008X-RAY DIFFRACTION99.27
2.05-2.090.23422210.17463867X-RAY DIFFRACTION99.3
2.09-2.130.21032060.17674004X-RAY DIFFRACTION99.29
2.13-2.170.23222270.183803X-RAY DIFFRACTION99.33
2.17-2.220.23672240.18293945X-RAY DIFFRACTION99.33
2.22-2.270.24852770.17253926X-RAY DIFFRACTION99.43
2.27-2.330.23422110.16853885X-RAY DIFFRACTION99.22
2.33-2.390.23832240.18823850X-RAY DIFFRACTION99.03
2.39-2.460.22991750.16143947X-RAY DIFFRACTION99.02
2.46-2.540.19461690.15154082X-RAY DIFFRACTION99.63
2.54-2.630.15821960.15623911X-RAY DIFFRACTION99.39
2.63-2.740.20611930.14763944X-RAY DIFFRACTION99.69
2.74-2.860.17722170.14493987X-RAY DIFFRACTION99.93
2.86-3.010.16682260.15073882X-RAY DIFFRACTION99.76
3.01-3.20.19371760.15713923X-RAY DIFFRACTION99.73
3.2-3.450.18131980.14543996X-RAY DIFFRACTION99.64
3.45-3.80.15552330.12873937X-RAY DIFFRACTION99.78
3.8-4.340.13961850.11633973X-RAY DIFFRACTION99.81
4.35-5.470.13572020.12163952X-RAY DIFFRACTION99.31
5.47-56.970.18162150.15813887X-RAY DIFFRACTION99.08

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