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

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Basic information

Entry
Database: PDB / ID: 7blg
TitleStructure of CBM BT3015C from Bacteroides thetaiotaomicron in complex with galactose
Componentsfamily 32 carbohydrate-binding module from Bacteroides thetaiotaomicron
KeywordsSUGAR BINDING PROTEIN / Bacteroides thetaiotaomicron / carbohydrate-binding module / gut microbiome / mucins / galactose
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
beta-D-galactopyranose / Carbohydrate-binding protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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)18,1383
Polymers17,9181
Non-polymers2202
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint2 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.853, 34.524, 47.746
Angle α, β, γ (deg.)90.000, 98.953, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
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: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.67 Å3/Da / Density % sol: 26.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 8mg/ml 0.12 M monosaccharides (0.2 M D Glucose; 0.2 M D Mannose; 0.2 M D Galactose; 0.2 M L Fucose; 0.2M D Xylose; 0.2 M N Acetyl D Glucosamine), 0.1 M buffer system (1.0 M pH 7.5 ...Details: Protein at 8mg/ml 0.12 M monosaccharides (0.2 M D Glucose; 0.2 M D Mannose; 0.2 M D Galactose; 0.2 M L Fucose; 0.2M D Xylose; 0.2 M N Acetyl D Glucosamine), 0.1 M buffer system (1.0 M pH 7.5 Sodium HEPES; MOPS) and 37.5% precipitant (25% v/v MPD; 25% w/v PEG 1000; 25% w/v PEG 3350)

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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: 1.17→36.4 Å / Num. obs: 35097 / % possible obs: 88.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.92 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.5
Reflection shellResolution: 1.17→1.19 Å / Num. unique obs: 1844 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4a41

4a41


Resolution: 1.18→36.4 Å / SU ML: 0.0967 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.7806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1738 1795 5.12 %
Rwork0.1574 33284 -
obs0.1582 35079 88.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.6 Å2
Refinement stepCycle: LAST / Resolution: 1.18→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 13 176 1297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491189
X-RAY DIFFRACTIONf_angle_d0.81691611
X-RAY DIFFRACTIONf_chiral_restr0.0866171
X-RAY DIFFRACTIONf_plane_restr0.0054211
X-RAY DIFFRACTIONf_dihedral_angle_d6.6691172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.23291440.2392680X-RAY DIFFRACTION93.67
1.21-1.240.26311390.23572687X-RAY DIFFRACTION93.79
1.24-1.280.23961110.22351973X-RAY DIFFRACTION68.64
1.28-1.330.20961490.20132724X-RAY DIFFRACTION95.2
1.33-1.380.1841530.19052704X-RAY DIFFRACTION94.85
1.38-1.450.19941530.17842762X-RAY DIFFRACTION95.86
1.45-1.520.21091170.16942037X-RAY DIFFRACTION78.7
1.53-1.620.18871400.16252645X-RAY DIFFRACTION95.47
1.62-1.740.16281320.1592565X-RAY DIFFRACTION88.14
1.74-1.920.16881560.15882816X-RAY DIFFRACTION97.76
1.92-2.20.19051470.14482833X-RAY DIFFRACTION97.87
2.2-2.770.18681130.15882098X-RAY DIFFRACTION72.11
2.77-36.40.14211410.13852760X-RAY DIFFRACTION92.18

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