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- PDB-6ef9: GspB Siglec domain -

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Basic information

Entry
Database: PDB / ID: 6ef9
TitleGspB Siglec domain
ComponentsPlatelet binding protein GspB - Siglec domain
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
FORMIC ACID / Platelet binding protein GspB
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
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 - Siglec domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,32012
Polymers13,9521
Non-polymers36811
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Platelet binding protein GspB - Siglec domain
hetero molecules

A: Platelet binding protein GspB - Siglec domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,64124
Polymers27,9052
Non-polymers73622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area4320 Å2
ΔGint-88 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.083, 92.083, 143.928
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-607-

FMT

21A-607-

FMT

31A-895-

HOH

41A-906-

HOH

51A-908-

HOH

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Components

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


Mass: 13952.391 Da / Num. of mol.: 1
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*PLUS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 4 M NaFormate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / 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: 1.3→50 Å / Num. obs: 57769 / % possible obs: 99.9 % / Redundancy: 13.8 % / Net I/σ(I): 59.3
Reflection shellResolution: 1.3→1.33 Å

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Processing

SoftwareName: PHENIX / Version: (1.12_2829) / Classification: refinement
RefinementResolution: 1.3→33.219 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1438 2000 3.47 %
Rwork0.1308 --
obs0.1313 57678 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→33.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 21 215 1171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081003
X-RAY DIFFRACTIONf_angle_d0.9811368
X-RAY DIFFRACTIONf_dihedral_angle_d17.19357
X-RAY DIFFRACTIONf_chiral_restr0.081158
X-RAY DIFFRACTIONf_plane_restr0.008180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33250.21151380.1893856X-RAY DIFFRACTION98
1.3325-1.36860.18911420.15883931X-RAY DIFFRACTION100
1.3686-1.40880.17221420.14223967X-RAY DIFFRACTION100
1.4088-1.45430.15071420.12233951X-RAY DIFFRACTION100
1.4543-1.50630.12791420.11663957X-RAY DIFFRACTION100
1.5063-1.56660.17571430.11633963X-RAY DIFFRACTION100
1.5666-1.63790.12071420.1153952X-RAY DIFFRACTION100
1.6379-1.72420.14451410.11763952X-RAY DIFFRACTION100
1.7242-1.83230.1371440.11924001X-RAY DIFFRACTION100
1.8323-1.97370.13941420.11743953X-RAY DIFFRACTION100
1.9737-2.17230.1271440.11224005X-RAY DIFFRACTION100
2.1723-2.48650.13251440.13144007X-RAY DIFFRACTION100
2.4865-3.13240.15431450.14464031X-RAY DIFFRACTION100
3.1324-33.22990.14211490.13774152X-RAY DIFFRACTION100

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