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- PDB-7blj: Structure of CBM BT3015C from Bacteroides thetaiotaomicron in com... -

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Basic information

Entry
Database: PDB / ID: 7blj
TitleStructure of CBM BT3015C from Bacteroides thetaiotaomicron in complex with O-GalNAc core 2-Thr
Componentsfamily 32 carbohydrate-binding module from Bacteroides thetaiotaomicron
KeywordsSUGAR BINDING PROTEIN / Bacteroides thetaiotaomicron / carbohydrate-binding module / gut microbiome / mucins / O-GalNAc core 2-Thr
Function / homology
Function and homology information


: / Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain ...: / Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold
Similarity search - Domain/homology
THREONINE / Carbohydrate-binding protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: family 32 carbohydrate-binding module from Bacteroides thetaiotaomicron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7255
Polymers17,9181
Non-polymers8084
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint13 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.541, 64.965, 70.603
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein family 32 carbohydrate-binding module from Bacteroides thetaiotaomicron


Mass: 17917.562 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_3015
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A3D9
#2: Polysaccharide beta-D-galactopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3[DGlcpNAcb1-6]DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}[(6+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 196 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 8mg/ml 0.1 M sodium citrate pH 5.0 and 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→23.37 Å / Num. obs: 16860 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 11.56 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 24
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.5 / Num. unique obs: 2538

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BLG

7blg


Resolution: 1.76→23.37 Å / SU ML: 0.2069 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 848 5.05 %
Rwork0.164 15952 -
obs0.1669 16800 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.1 Å2
Refinement stepCycle: LAST / Resolution: 1.76→23.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 52 193 1353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631233
X-RAY DIFFRACTIONf_angle_d0.88941668
X-RAY DIFFRACTIONf_chiral_restr0.0625184
X-RAY DIFFRACTIONf_plane_restr0.0063215
X-RAY DIFFRACTIONf_dihedral_angle_d7.6804180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.870.30511400.22412590X-RAY DIFFRACTION99.38
1.87-2.010.26051470.18842601X-RAY DIFFRACTION99.89
2.01-2.220.21591400.15832628X-RAY DIFFRACTION100
2.22-2.540.23421330.16412662X-RAY DIFFRACTION100
2.54-3.190.19971380.1642672X-RAY DIFFRACTION100
3.2-23.370.19531500.14392799X-RAY DIFFRACTION99.97

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