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- PDB-7kmj: Hsa Siglec and Unique domains in complex with Sialyl Lewis C -

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Basic information

Entry
Database: PDB / ID: 7kmj
TitleHsa Siglec and Unique domains in complex with Sialyl Lewis C
ComponentsStreptococcal hemagglutinin
KeywordsCELL ADHESION / adhesin
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 / 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
Similarity search - Domain/homology
Streptococcal hemagglutinin
Similarity search - Component
Biological speciesStreptococcus gordonii str. Challis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsStubbs, H.E. / Iverson, T.M.
Funding support3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
American Heart Association
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
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
DepositionNov 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)26,5815
Polymers25,8371
Non-polymers7444
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.635, 58.173, 75.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Streptococcal hemagglutinin / Hs antigen / Sialic acid-binding adhesin


Mass: 25837.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii str. Challis (bacteria)
Strain: Challis / Gene: hsa, SGO_0966 / Production host: Escherichia coli (E. coli) / References: UniProt: A8AWU7
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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, sitting drop
Details: 21.6 mg/ml in 20 mM Tris-HCl, pH 7.2. Equilibrate 1 ul protein and 2 ul reservoir solution over 50 ul of reservoir solution (0.1 M Succinate/Phosphate/Glycine pH 10.0 and 25% PEG 3350). ...Details: 21.6 mg/ml in 20 mM Tris-HCl, pH 7.2. Equilibrate 1 ul protein and 2 ul reservoir solution over 50 ul of reservoir solution (0.1 M Succinate/Phosphate/Glycine pH 10.0 and 25% PEG 3350). Crystals were soaked in reservoir solution supplemented with 5 mM of sLec for 20 hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 1748709 / % possible obs: 99.7 % / Redundancy: 8 % / Biso Wilson estimate: 16.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 40.5
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 2468 / CC1/2: 0.891

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EQ2

5eq2


Resolution: 1.33→37.99 Å / SU ML: 0.1624 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6886
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 2402 5.01 %
Rwork0.1911 45536 -
obs0.1924 47938 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.33→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 49 280 1909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01231690
X-RAY DIFFRACTIONf_angle_d1.50992315
X-RAY DIFFRACTIONf_chiral_restr0.0985272
X-RAY DIFFRACTIONf_plane_restr0.0161303
X-RAY DIFFRACTIONf_dihedral_angle_d12.4213625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.360.42141370.35122593X-RAY DIFFRACTION98.77
1.36-1.390.32241390.30182629X-RAY DIFFRACTION98.82
1.39-1.420.28331380.26292640X-RAY DIFFRACTION99.39
1.42-1.450.25821410.23152651X-RAY DIFFRACTION99.15
1.45-1.490.2541390.23382625X-RAY DIFFRACTION99.07
1.49-1.540.26371350.21392645X-RAY DIFFRACTION99.39
1.54-1.590.25951410.20842645X-RAY DIFFRACTION98.9
1.59-1.640.25061390.20892642X-RAY DIFFRACTION99.64
1.64-1.710.25251410.20492677X-RAY DIFFRACTION99.47
1.71-1.790.23491420.1952652X-RAY DIFFRACTION99.4
1.79-1.880.20511410.18572681X-RAY DIFFRACTION99.86
1.88-20.22691410.18092675X-RAY DIFFRACTION99.65
2-2.150.21531430.18812703X-RAY DIFFRACTION99.96
2.15-2.370.23511420.17282696X-RAY DIFFRACTION99.93
2.37-2.710.21261440.18762738X-RAY DIFFRACTION99.93
2.71-3.420.19711480.18242765X-RAY DIFFRACTION99.9
3.42-37.990.18131510.1782879X-RAY DIFFRACTION99.9

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