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- PDB-9bam: Surface glycan-binding protein A (SGBP-A, SusD-like) from a mixed... -

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Basic information

Entry
Database: PDB / ID: 9bam
TitleSurface glycan-binding protein A (SGBP-A, SusD-like) from a mixed-linkage beta-glucan utilization locus in Segatella copri
ComponentsSurface glycan-binding protein A (SGBP-A)
KeywordsSUGAR BINDING PROTEIN / glycan-binding protein / SGBP-A / mixed-linkage beta-glucan / Segatella copri
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Uncharacterized protein
Function and homology information
Biological speciesSegatella copri DSM 18205 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCordeiro, R.L. / Golisch, B. / Brumer, H. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The molecular basis of cereal mixed-linkage beta-glucan utilization by the human gut bacterium Segatella copri.
Authors: Golisch, B. / Cordeiro, R.L. / Fraser, A.S.C. / Briggs, J. / Stewart, W.A. / Van Petegem, F. / Brumer, H.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Surface glycan-binding protein A (SGBP-A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1982
Polymers67,1741
Non-polymers241
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.877, 76.849, 99.918
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 Surface glycan-binding protein A (SGBP-A)


Mass: 67174.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Segatella copri DSM 18205 (bacteria) / Gene: PREVCOP_05098 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D1PD12
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.5) and 26% (w/v) Polyethylene glycol (PEG) 8,000
Temp details: Room temperature

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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 EIGER X 16M / Detector: PIXEL / Date: May 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→33.56 Å / Num. obs: 33784 / % possible obs: 99.31 % / Redundancy: 2 % / Biso Wilson estimate: 27.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0449 / Net I/σ(I): 8.41
Reflection shellResolution: 2.05→2.123 Å / Rmerge(I) obs: 0.2893 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 3338 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→33.56 Å / SU ML: 0.2884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7793
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 2558 4.02 %
Rwork0.1853 61046 -
obs0.1872 33784 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.15 Å2
Refinement stepCycle: LAST / Resolution: 2.05→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 1 204 4501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074430
X-RAY DIFFRACTIONf_angle_d0.84776024
X-RAY DIFFRACTIONf_chiral_restr0.0464621
X-RAY DIFFRACTIONf_plane_restr0.0081800
X-RAY DIFFRACTIONf_dihedral_angle_d5.7767603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.35871420.27573402X-RAY DIFFRACTION99.16
2.09-2.130.3231410.25813383X-RAY DIFFRACTION98.08
2.13-2.180.28891370.25083365X-RAY DIFFRACTION98.4
2.18-2.230.29361470.2343412X-RAY DIFFRACTION99.72
2.23-2.280.3161390.22973407X-RAY DIFFRACTION99.41
2.28-2.350.26361450.21873395X-RAY DIFFRACTION99.35
2.35-2.420.29021420.2113405X-RAY DIFFRACTION99.75
2.42-2.490.3141400.20593401X-RAY DIFFRACTION99.24
2.49-2.580.29261440.20143449X-RAY DIFFRACTION98.93
2.58-2.690.22381420.20283338X-RAY DIFFRACTION98.61
2.69-2.810.24351410.19263403X-RAY DIFFRACTION99.38
2.81-2.960.22191450.19143432X-RAY DIFFRACTION99.31
2.96-3.140.24591400.18223400X-RAY DIFFRACTION99.38
3.14-3.380.19441420.17183360X-RAY DIFFRACTION98.76
3.38-3.720.22131440.15893399X-RAY DIFFRACTION99.08
3.72-4.260.15151420.13993408X-RAY DIFFRACTION99.05
4.26-5.360.18981410.16353314X-RAY DIFFRACTION97.21
5.37-33.560.24171440.17133373X-RAY DIFFRACTION98.08
Refinement TLS params.Method: refined / Origin x: -16.9458993826 Å / Origin y: 16.4927621231 Å / Origin z: -22.3935806108 Å
111213212223313233
T0.217091160053 Å2-0.0190927184757 Å20.00599849988049 Å2-0.227193665136 Å20.00152173577047 Å2--0.217143385241 Å2
L0.566337972539 °20.0771795625767 °20.0531792612275 °2-0.581590121284 °20.139225439669 °2--0.394519670163 °2
S0.0214588777923 Å °-0.0583458562917 Å °-0.0121006858235 Å °-0.0141538655011 Å °-0.00517567272737 Å °-0.0862021535676 Å °-0.0364696017078 Å °0.0883234248397 Å °2.15376308917E-5 Å °
Refinement TLS groupSelection details: all

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