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- PDB-6efc: Hsa Siglec + Unique domains (unliganded) -

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Basic information

Entry
Database: PDB / ID: 6efc
TitleHsa Siglec + Unique domains (unliganded)
ComponentsStreptococcal hemagglutinin
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology
Function and homology information


surface biofilm formation / biofilm matrix assembly / cell adhesion / extracellular region
Similarity search - Function
SrpA-like, SigLec-like domain / GspA/SrpA SigLec-like domain / 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. ...SrpA-like, SigLec-like domain / GspA/SrpA SigLec-like domain / 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 / Alpha Beta
Similarity search - Domain/homology
Streptococcal hemagglutinin / Streptococcal hemagglutinin
Similarity search - Component
Biological speciesStreptococcus gordonii str. Challis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 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: Streptococcal hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9003
Polymers25,8371
Non-polymers632
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.635, 58.173, 75.973
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 Streptococcal hemagglutinin


Mass: 25837.381 Da / Num. of mol.: 1 / Fragment: residues 220-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii str. Challis (bacteria)
Gene: hsa / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWR3, UniProt: A8AWU7*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M SPG pH 10.0, 25% PEG3350

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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 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 39091 / % possible obs: 93.3 % / Redundancy: 12.6 % / Net I/σ(I): 49.7
Reflection shellResolution: 1.4→1.43 Å

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Processing

SoftwareName: PHENIX / Version: (1.14_3211) / Classification: refinement
RefinementResolution: 1.4→29.452 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 1958 5.01 %
Rwork0.1455 --
obs0.1472 39072 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→29.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 2 337 1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091684
X-RAY DIFFRACTIONf_angle_d1.1742319
X-RAY DIFFRACTIONf_dihedral_angle_d13.534635
X-RAY DIFFRACTIONf_chiral_restr0.091263
X-RAY DIFFRACTIONf_plane_restr0.007317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4350.2583920.19821740X-RAY DIFFRACTION63
1.435-1.47380.28861080.18172050X-RAY DIFFRACTION74
1.4738-1.51720.22381270.1662412X-RAY DIFFRACTION87
1.5172-1.56620.20361440.15092734X-RAY DIFFRACTION98
1.5662-1.62210.17351470.13242757X-RAY DIFFRACTION100
1.6221-1.68710.18381470.1292778X-RAY DIFFRACTION100
1.6871-1.76390.18281470.12552797X-RAY DIFFRACTION100
1.7639-1.85680.18821460.13262787X-RAY DIFFRACTION100
1.8568-1.97310.19761470.13052787X-RAY DIFFRACTION100
1.9731-2.12550.18861490.13212824X-RAY DIFFRACTION100
2.1255-2.33930.1841480.12962819X-RAY DIFFRACTION100
2.3393-2.67760.14751490.14112826X-RAY DIFFRACTION100
2.6776-3.37270.18221520.15232867X-RAY DIFFRACTION100
3.3727-29.45880.16671550.15772936X-RAY DIFFRACTION98

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