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- PDB-7k44: SGBP-B from a complex xyloglucan utilization locus in Bacteroides... -

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Basic information

Entry
Database: PDB / ID: 7k44
TitleSGBP-B from a complex xyloglucan utilization locus in Bacteroides uniformis
ComponentsSGBP-B
KeywordsSUGAR BINDING PROTEIN / surface glycan-binding protein / polysaccharide utilization locus
Function / homologySurface glycan-binding protein B, xyloglucan binding domain / Surface glycan-binding protein B xyloglucan binding domain / IPT/TIG domain / IPT domain / polysaccharide binding / Immunoglobulin E-set / Immunoglobulin-like fold / metal ion binding / IPT/TIG domain-containing protein
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBrumer, H. / Van Petegem, F. / Grondin, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Appl.Environ.Microbiol. / Year: 2022
Title: Cell Surface Xyloglucan Recognition and Hydrolysis by the Human Gut Commensal Bacteroides uniformis.
Authors: Grondin, J.M. / Dejean, G. / Van Petegem, F. / Brumer, H.
History
DepositionSep 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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: SGBP-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6542
Polymers42,6141
Non-polymers401
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.864, 66.718, 57.966
Angle α, β, γ (deg.)90.000, 115.238, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

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Components

#1: Protein SGBP-B


Mass: 42614.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (strain ATCC 8492 / DSM 6597 / CIP 103695 / JCM 5828 / NCTC 13054 / VPI 0061) (bacteria)
Strain: ATCC 8492 / DSM 6597 / CIP 103695 / JCM 5828 / NCTC 13054 / VPI 0061
Gene: BACUNI_03801 / Production host: Escherichia coli (E. coli) / References: UniProt: A7V885
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium chloride, 0.1M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.45→34.85 Å / Num. obs: 72049 / % possible obs: 99.17 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.04 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05159 / Rpim(I) all: 0.02169 / Rrim(I) all: 0.05606 / Net I/σ(I): 15.92
Reflection shellResolution: 1.45→1.506 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.515 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 41563 / CC1/2: 0.43 / CC star: 0.776 / Rpim(I) all: 0.6697 / Rrim(I) all: 1.66 / % possible all: 97.85

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E7G

5e7g


Resolution: 1.45→34.85 Å / SU ML: 0.2071 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2064 3566 4.95 %
Rwork0.1785 68463 -
obs0.1799 72029 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.45 Å2
Refinement stepCycle: LAST / Resolution: 1.45→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 1 368 3109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532885
X-RAY DIFFRACTIONf_angle_d0.78363963
X-RAY DIFFRACTIONf_chiral_restr0.084445
X-RAY DIFFRACTIONf_plane_restr0.0047517
X-RAY DIFFRACTIONf_dihedral_angle_d16.5465402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.40311250.40042648X-RAY DIFFRACTION97.26
1.47-1.490.34711500.35832716X-RAY DIFFRACTION98.25
1.49-1.520.32971660.31392677X-RAY DIFFRACTION98.27
1.52-1.540.28061310.28472678X-RAY DIFFRACTION98.46
1.54-1.570.30581550.26282732X-RAY DIFFRACTION98.57
1.57-1.590.28351470.25132700X-RAY DIFFRACTION98.72
1.59-1.620.26231290.24462739X-RAY DIFFRACTION98.73
1.62-1.650.26141320.2282716X-RAY DIFFRACTION98.82
1.65-1.690.23791200.21352732X-RAY DIFFRACTION98.79
1.69-1.720.22861230.21122748X-RAY DIFFRACTION99.17
1.72-1.760.20121320.21132762X-RAY DIFFRACTION99.18
1.76-1.810.28461320.21262742X-RAY DIFFRACTION99.21
1.81-1.860.23181200.20122753X-RAY DIFFRACTION99.52
1.86-1.910.21531500.19162760X-RAY DIFFRACTION99.56
1.91-1.970.21331270.19182737X-RAY DIFFRACTION99.51
1.97-2.040.21851440.18842751X-RAY DIFFRACTION99.72
2.04-2.130.22331660.19652716X-RAY DIFFRACTION99.69
2.13-2.220.23381750.18742732X-RAY DIFFRACTION99.66
2.22-2.340.22731540.18652741X-RAY DIFFRACTION99.79
2.34-2.490.2381450.1942765X-RAY DIFFRACTION99.93
2.49-2.680.22741470.1872767X-RAY DIFFRACTION99.9
2.68-2.950.23881380.18872773X-RAY DIFFRACTION99.76
2.95-3.370.20771500.16832772X-RAY DIFFRACTION99.66
3.37-4.250.16951580.14122771X-RAY DIFFRACTION99.66
4.25-34.850.13941500.13952835X-RAY DIFFRACTION99.53

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