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- PDB-6efb: GspB Siglec domain -

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Basic information

Entry
Database: PDB / ID: 6efb
TitleGspB Siglec domain
ComponentsSK150 siglec + Unique
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homologyImmunoglobulin-like - #4140 / Ubiquitin-like (UB roll) - #890 / Ubiquitin-like (UB roll) / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 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: SK150 siglec + Unique
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7474
Polymers23,5191
Non-polymers2283
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.270, 62.580, 62.930
Angle α, β, γ (deg.)90.00, 98.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SK150 siglec + Unique


Mass: 23518.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonim sulfate, 25% PEG 4000, 15% ethanol. 0.1 M Bis-tris pH 7.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.542 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 14767 / % possible obs: 97.3 % / Redundancy: 9 % / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→1.94 Å

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Processing

SoftwareName: PHENIX / Version: (1.11.1_2575) / Classification: refinement
RefinementResolution: 1.9→23.606 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 704 5.06 %
Rwork0.17 --
obs0.1708 13926 94.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→23.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 12 142 1704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061649
X-RAY DIFFRACTIONf_angle_d0.742246
X-RAY DIFFRACTIONf_dihedral_angle_d15.628611
X-RAY DIFFRACTIONf_chiral_restr0.054254
X-RAY DIFFRACTIONf_plane_restr0.005302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.04670.25341130.2162372X-RAY DIFFRACTION84
2.0467-2.25250.21031280.19172546X-RAY DIFFRACTION91
2.2525-2.57810.19031470.1842719X-RAY DIFFRACTION97
2.5781-3.24680.21181460.1722762X-RAY DIFFRACTION99
3.2468-23.6080.1531700.14552823X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -5.9764 Å / Origin y: -0.8306 Å / Origin z: 14.5766 Å
111213212223313233
T0.0824 Å20.0006 Å2-0.0016 Å2-0.0736 Å20.0035 Å2--0.1032 Å2
L0.6162 °20.042 °20.1961 °2-0.5139 °2-0.1457 °2--1.1721 °2
S-0.0234 Å °0.1327 Å °0.0666 Å °-0.1042 Å °0.0156 Å °0.0366 Å °-0.0786 Å °0.0962 Å °-0.004 Å °
Refinement TLS groupSelection details: all

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