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- PDB-6ef7: GspB Siglec domain -

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Basic information

Entry
Database: PDB / ID: 6ef7
TitleGspB Siglec domain
ComponentsPlatelet binding protein GspB
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
Immunoglobulin-like - #4140 / 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 ...Immunoglobulin-like - #4140 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Platelet binding protein GspB
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.03 Å
AuthorsIverson, T.M.
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

Downloads & links

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Assembly

Deposited unit
A: Platelet binding protein GspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9922
Polymers13,9521
Non-polymers401
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.920, 46.210, 72.970
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: 13952.391 Da / Num. of mol.: 1 / Fragment: Ser-rich 2 (SSR2) siglec domain residues 399-521
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.: 246 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
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: 1.03→50 Å / Num. obs: 54763 / % possible obs: 95.4 % / Redundancy: 9.3 % / Net I/σ(I): 25.5
Reflection shellResolution: 1.03→1.06 Å

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Processing

SoftwareName: PHENIX / Version: (1.12_2829) / Classification: refinement
RefinementResolution: 1.03→39.04 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1413 2767 5.06 %
Rwork0.1253 --
obs0.1261 54668 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.03→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 1 246 1209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081061
X-RAY DIFFRACTIONf_angle_d1.011465
X-RAY DIFFRACTIONf_dihedral_angle_d14.685379
X-RAY DIFFRACTIONf_chiral_restr0.083170
X-RAY DIFFRACTIONf_plane_restr0.008197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.04780.17851170.15262437X-RAY DIFFRACTION90
1.0478-1.06680.14721410.13162462X-RAY DIFFRACTION91
1.0668-1.08740.16561360.12032474X-RAY DIFFRACTION92
1.0874-1.10960.13311430.11132465X-RAY DIFFRACTION92
1.1096-1.13370.12071520.10232494X-RAY DIFFRACTION93
1.1337-1.16010.13411330.09742527X-RAY DIFFRACTION93
1.1601-1.18910.11041340.09952516X-RAY DIFFRACTION94
1.1891-1.22120.13411570.09842514X-RAY DIFFRACTION94
1.2212-1.25720.12921120.10042555X-RAY DIFFRACTION94
1.2572-1.29770.12851380.10772578X-RAY DIFFRACTION96
1.2977-1.34410.12551600.10692557X-RAY DIFFRACTION95
1.3441-1.3980.13521390.10432592X-RAY DIFFRACTION96
1.398-1.46160.11051520.10222607X-RAY DIFFRACTION96
1.4616-1.53860.12181360.10432628X-RAY DIFFRACTION96
1.5386-1.6350.11741200.10762688X-RAY DIFFRACTION97
1.635-1.76130.13911310.11852670X-RAY DIFFRACTION97
1.7613-1.93850.13591390.12762700X-RAY DIFFRACTION98
1.9385-2.2190.12541160.12312768X-RAY DIFFRACTION98
2.219-2.79560.15281430.15062776X-RAY DIFFRACTION99
2.7956-39.06820.17261680.15522893X-RAY DIFFRACTION99

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