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- PDB-9q3h: GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC -

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Basic information

Entry
Database: PDB / ID: 9q3h
TitleGspB Siglec domain bound to sialyl T antigen linked to serine-FMOC
ComponentsPlatelet binding protein GspB
KeywordsSUGAR BINDING PROTEIN / SLBR
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
Atypical Rib domain / Atypical Rib domain / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / : / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
SERINE / : / Platelet binding protein GspB
Similarity search - Component
Biological speciesStreptococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMorrison, K.M. / Martin, K.A. / Iverson, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC
Authors: Morrison, K.M. / Martin, K.A. / Iverson, T.M.
History
DepositionAug 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Platelet binding protein GspB
B: Platelet binding protein GspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,24612
Polymers27,9052
Non-polymers2,34110
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.987, 38.111, 47.054
Angle α, β, γ (deg.)70.200, 68.010, 62.080
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Platelet binding protein GspB / Adhesin GspB / Serine-rich adhesin for platelets / Serine-rich repeat protein GspB


Mass: 13952.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus (bacteria) / Gene: gspB / Production host: Escherichia coli (E. coli) / References: UniProt: Q939N5
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[]{[(3+?)][<C8N1O3>]{[(1+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 141 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VP1 / Fluorenylmethyloxycarbonyl chloride


Mass: 258.700 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11ClO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 1 uL protein (22 mg/ml preincubated in 10 mM sTa-Ser-FMOC) and 2 uL reservoir solution over 600 uL reservoir solution ( 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, 50% PEG 4000). Crystals were ...Details: 1 uL protein (22 mg/ml preincubated in 10 mM sTa-Ser-FMOC) and 2 uL reservoir solution over 600 uL reservoir solution ( 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, 50% PEG 4000). Crystals were cryoprotected in 25% (v/v) glycerol and flash-cooled in liquid nitrogen. protein was in 18 mM Tris-HCl, pH 7.5, and 200 mM NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.89→23.1 Å / Num. obs: 14353 / % possible obs: 86 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.184 / Rsym value: 0.065 / Net I/σ(I): 26.2
Reflection shellResolution: 1.89→1.93 Å / Num. unique obs: 2360 / CC1/2: 0.981 / Rsym value: 0.218 / % possible all: 63.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-20001.20_4459data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→23.1 Å / SU ML: 0.1843 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 23.6279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2109 711 4.95 %
Rwork0.1837 13642 -
obs0.1851 14353 84.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.12 Å2
Refinement stepCycle: LAST / Resolution: 1.89→23.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 152 133 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512141
X-RAY DIFFRACTIONf_angle_d0.73942930
X-RAY DIFFRACTIONf_chiral_restr0.0545346
X-RAY DIFFRACTIONf_plane_restr0.005371
X-RAY DIFFRACTIONf_dihedral_angle_d13.539738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-2.040.24061310.19932360X-RAY DIFFRACTION73.63
2.04-2.240.27111390.19762757X-RAY DIFFRACTION84.85
2.24-2.560.21411460.20852809X-RAY DIFFRACTION87.82
2.56-3.230.24311520.20292830X-RAY DIFFRACTION87.89
3.23-23.10.17291430.16152886X-RAY DIFFRACTION89.17

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