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- PDB-6efa: GspB Siglec + Unique domains -

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Basic information

Entry
Database: PDB / ID: 6efa
TitleGspB Siglec + Unique domains
ComponentsPlatelet binding protein GspB
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
Immunoglobulin-like - #4140 / : / Ubiquitin-like (UB roll) - #890 / 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. ...Immunoglobulin-like - #4140 / : / Ubiquitin-like (UB roll) - #890 / 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 / Ubiquitin-like (UB roll) / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Platelet binding protein GspB
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsIverson, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106987 United States
CitationJournal: Nat Commun / Year: 2022
Title: Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation.
Authors: Bensing, B.A. / Stubbs, H.E. / Agarwal, R. / Yamakawa, I. / Luong, K. / Solakyildirim, K. / Yu, H. / Hadadianpour, A. / Castro, M.A. / Fialkowski, K.P. / Morrison, K.M. / Wawrzak, Z. / Chen, ...Authors: Bensing, B.A. / Stubbs, H.E. / Agarwal, R. / Yamakawa, I. / Luong, K. / Solakyildirim, K. / Yu, H. / Hadadianpour, A. / Castro, M.A. / Fialkowski, K.P. / Morrison, K.M. / Wawrzak, Z. / Chen, X. / Lebrilla, C.B. / Baudry, J. / Smith, J.C. / Sullam, P.M. / Iverson, T.M.
History
DepositionAug 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Platelet binding protein GspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8172
Polymers22,7771
Non-polymers401
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.980, 47.630, 136.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22777.246 Da / Num. of mol.: 1 / Fragment: Ser-rich 2 (SSR2) siglec domain residues 399-601
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Gene: gspB / Production host: Escherichia coli (E. coli) / References: UniProt: Q939N5
#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.: 304 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 29333 / % possible obs: 88.9 % / Redundancy: 9.2 % / Net I/σ(I): 43.8
Reflection shellResolution: 1.6→1.64 Å

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Processing

SoftwareName: PHENIX / Version: dev_1951 / Classification: refinement
RefinementResolution: 1.6→39.034 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.76
RfactorNum. reflection% reflection
Rfree0.2116 2310 8.89 %
Rwork0.1631 --
obs0.1673 25981 88.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→39.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 1 304 1874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171620
X-RAY DIFFRACTIONf_angle_d1.6042207
X-RAY DIFFRACTIONf_dihedral_angle_d12.339591
X-RAY DIFFRACTIONf_chiral_restr0.095259
X-RAY DIFFRACTIONf_plane_restr0.011290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5986-1.63340.2829760.215754X-RAY DIFFRACTION46
1.6334-1.67140.2613970.205962X-RAY DIFFRACTION59
1.6714-1.71320.25911250.17811231X-RAY DIFFRACTION75
1.7132-1.75950.26951360.17621412X-RAY DIFFRACTION85
1.7595-1.81130.23421330.17691430X-RAY DIFFRACTION87
1.8113-1.86970.2481420.17941461X-RAY DIFFRACTION90
1.8697-1.93650.25151500.17621521X-RAY DIFFRACTION92
1.9365-2.01410.21451510.16751554X-RAY DIFFRACTION96
2.0141-2.10570.22251510.16271588X-RAY DIFFRACTION95
2.1057-2.21670.23781590.16111619X-RAY DIFFRACTION97
2.2167-2.35560.23971610.16591630X-RAY DIFFRACTION98
2.3556-2.53750.20831600.17131663X-RAY DIFFRACTION98
2.5375-2.79270.21511620.16771656X-RAY DIFFRACTION99
2.7927-3.19670.19821630.17011680X-RAY DIFFRACTION100
3.1967-4.02690.19581660.14541710X-RAY DIFFRACTION100
4.0269-39.04580.18511780.15611800X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 44.626 Å / Origin y: 102.1303 Å / Origin z: 18.2928 Å
111213212223313233
T0.1512 Å2-0.0182 Å20.0084 Å2-0.1455 Å2-0.0028 Å2--0.1631 Å2
L0.6104 °2-0.3085 °20.1078 °2-0.71 °20.0898 °2--0.337 °2
S-0.0496 Å °-0.0913 Å °-0.0449 Å °0.1391 Å °0.0163 Å °0.0511 Å °0.1406 Å °-0.023 Å °-0 Å °
Refinement TLS groupSelection details: all

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