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- PDB-7kwb: Surface glycan-binding protein B from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 7kwb
TitleSurface glycan-binding protein B from Bacteroides thetaiotaomicron
ComponentsBtSGBP-B
KeywordsSUGAR BINDING PROTEIN / CBM / lectin
Function / homologyPKD domain superfamily / Galactose-binding-like domain superfamily / DUF5017 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsTamura, K. / Brumer, H. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota.
Authors: Tamura, K. / Dejean, G. / Van Petegem, F. / Brumer, H.
History
DepositionNov 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BtSGBP-B
B: BtSGBP-B


Theoretical massNumber of molelcules
Total (without water)101,5052
Polymers101,5052
Non-polymers00
Water1,56787
1
A: BtSGBP-B


Theoretical massNumber of molelcules
Total (without water)50,7521
Polymers50,7521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BtSGBP-B


Theoretical massNumber of molelcules
Total (without water)50,7521
Polymers50,7521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.101, 182.141, 92.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BtSGBP-B


Mass: 50752.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: HMPREF2534_00387 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A139L065
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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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: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 0.1M HEPES pH7.4, 1.3M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→39.4 Å / Num. obs: 45378 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 17
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 4409 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→39.4 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.798 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2865 2199 4.8 %RANDOM
Rwork0.2384 ---
obs0.2407 43158 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.03 Å2 / Biso mean: 69.559 Å2 / Biso min: 32.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å20 Å20 Å2
2---1.25 Å20 Å2
3----2.3 Å2
Refinement stepCycle: final / Resolution: 2.6→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6121 0 0 87 6208
Biso mean---50.94 -
Num. residues----812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136274
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175376
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.6398607
X-RAY DIFFRACTIONr_angle_other_deg1.0971.57112464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.485807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32625.477283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66615868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.266157
X-RAY DIFFRACTIONr_chiral_restr0.0350.2897
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021266
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 163 -
Rwork0.316 3117 -
all-3280 -
obs--99.91 %

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