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- PDB-7blk: Structure of CBM BT3015C from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 7blk
TitleStructure of CBM BT3015C from Bacteroides thetaiotaomicron
Componentsfamily 32 carbohydrate-binding module from Bacteroides thetaiotaomicron
KeywordsSUGAR BINDING PROTEIN / Bacteroides thetaiotaomicron / carbohydrate-binding module / gut microbiome / mucins
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
Carbohydrate-binding protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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)17,9582
Polymers17,9181
Non-polymers401
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.682, 34.291, 47.587
Angle α, β, γ (deg.)90.000, 98.920, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 (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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.65 Å3/Da / Density % sol: 25.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8 mg/ml 30% w/v PEG 2000 monomethyl ether and 0.1 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.06→36.24 Å / Num. obs: 84450 / % possible obs: 98.6 % / Redundancy: 3 % / Biso Wilson estimate: 12.64 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.5
Reflection shellResolution: 1.06→1.08 Å / Num. unique obs: 2611 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BLG

7blg


Resolution: 1.06→36.24 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1748 4044 4.79 %
Rwork0.1682 80406 -
obs0.1685 84450 81.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.23 Å2 / Biso mean: 16.6276 Å2 / Biso min: 8.86 Å2
Refinement stepCycle: final / Resolution: 1.06→36.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 1 186 1291
Biso mean--10.81 25.34 -
Num. residues----142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.06-1.070.27541460.25912660280676
1.07-1.090.27971290.24972550267976
1.09-1.10.22431580.23912580273877
1.1-1.110.26191290.23242650277977
1.11-1.130.27171050.2172608271376
1.13-1.140.21991490.21482627277676
1.14-1.160.18311270.21242654278179
1.16-1.180.20331530.20882719287280
1.18-1.20.211240.21212685280979
1.2-1.220.21481530.20362806295980
1.22-1.240.22431330.2082694282780
1.24-1.270.19061420.2012804294681
1.27-1.290.21841200.19732729284980
1.29-1.320.19951170.20012869298682
1.32-1.350.22151750.19142801297683
1.35-1.380.17821300.18812823295383
1.38-1.420.20831440.18272891303583
1.42-1.460.17981420.18742803294583
1.46-1.510.20811290.17352837296683
1.51-1.570.17591580.17752780293882
1.57-1.630.17511490.17622893304284
1.63-1.70.14631320.17162856298884
1.7-1.790.18821410.18132880302183
1.79-1.90.17361180.17692829294782
1.9-2.050.18621190.16182812293182
2.05-2.260.19571400.16182843298383
2.26-2.580.17481590.16422845300484
2.58-3.250.16321840.16382855303985
3.25-36.240.12431390.13133023316288

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