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

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Basic information

Entry
Database: PDB / ID: 7blh
TitleStructure of CBM BT3015C from Bacteroides thetaiotaomicron in complex with O-GalNAc core 1-Thr
Componentsfamily 32 carbohydrate-binding module from Bacteroides thetaiotaomicron
KeywordsSUGAR BINDING PROTEIN / Bacteroides thetaiotaomicron / carbohydrate-binding module / gut microbiome / mucins / O-GalNAc core 1-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 VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsCosta, R.L. / Carvalho, A.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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,4604
Polymers17,9181
Non-polymers5433
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint7 kcal/mol
Surface area7230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.525, 64.011, 70.211
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

#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 VPI-5482 (bacteria)
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-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 8mg/ml 0.2 M potassium formate 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 IMUS MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→23.65 Å / Num. obs: 15596 / % possible obs: 99.2 % / Redundancy: 5.82 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.09
Reflection shellResolution: 1.79→1.89 Å / Rmerge(I) obs: 0.256 / Num. unique obs: 2194

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Processing

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

7blg


Resolution: 1.79→20.42 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.283
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2027 643 4.83 %
Rwork0.1568 12680 -
obs0.159 13323 85.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.92 Å2
Refinement stepCycle: LAST / Resolution: 1.79→20.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 34 233 1375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671166
X-RAY DIFFRACTIONf_angle_d0.85591571
X-RAY DIFFRACTIONf_chiral_restr0.0628170
X-RAY DIFFRACTIONf_plane_restr0.005202
X-RAY DIFFRACTIONf_dihedral_angle_d7.0634162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.930.2428930.18211828X-RAY DIFFRACTION62.86
1.93-2.120.202950.15872393X-RAY DIFFRACTION80.7
2.12-2.430.2231250.15842553X-RAY DIFFRACTION86.75
2.43-3.060.20271670.16242820X-RAY DIFFRACTION95.01
3.06-20.420.18461630.14623086X-RAY DIFFRACTION99.15

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