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- PDB-5eq3: Crystal structure of the SrpA adhesin from Streptococcus sanguini... -

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Basic information

Entry
Database: PDB / ID: 5eq3
TitleCrystal structure of the SrpA adhesin from Streptococcus sanguinis with a sialyl galactose disaccharide bound
ComponentsPlatelet-binding glycoprotein
KeywordsSUGAR BINDING PROTEIN / bacterial adhesin / lectin / immunoglobulin fold / serine-rich repeat
Function / homology
Function and homology information


extracellular region / metal ion binding
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
ACETATE ION / Platelet-binding glycoprotein
Similarity search - Component
Biological speciesStreptococcus sanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLoukachevitch, L.V. / McCulloch, K.M. / Vann, K.R. / Wawrzak, Z. / Anderson, S. / Iverson, T.M.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106987 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI41513 United States
Department of Veteran's Affairs United States
American Heart Association14GRNT20390021 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008320 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32 HL007751 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR026915 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Michigan Economic Development Corporation085P1000817 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Sialoglycan Binding by the Streptococcus sanguinis SrpA Adhesin.
Authors: Bensing, B.A. / Loukachevitch, L.V. / McCulloch, K.M. / Yu, H. / Vann, K.R. / Wawrzak, Z. / Anderson, S. / Chen, X. / Sullam, P.M. / Iverson, T.M.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Platelet-binding glycoprotein
B: Platelet-binding glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,07314
Polymers44,0912
Non-polymers98212
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-46 kcal/mol
Surface area20410 Å2
MethodPISA
2
A: Platelet-binding glycoprotein
B: Platelet-binding glycoprotein
hetero molecules

A: Platelet-binding glycoprotein
B: Platelet-binding glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,14628
Polymers88,1814
Non-polymers1,96424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6110 Å2
ΔGint-104 kcal/mol
Surface area39750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.620, 47.005, 64.026
Angle α, β, γ (deg.)90.000, 102.150, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

21B-728-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Platelet-binding glycoprotein


Mass: 22045.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis (bacteria) / Strain: SK36 / Gene: srpA, SSA_0829 / Plasmid: pGEX3X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: A3CM52
#2: Polysaccharide N-glycolyl-alpha-neuraminic acid-(2-3)-methyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 501.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Gca2-3DGalp[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OC][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Galp]{[(3+2)][a-D-Neup5Gc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 357 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Na cacodylate, 0.2 M Ca(CH3CO2)2, 18% PEG 8000. SrpA protein was concentrated to 16 mg/mL in 20 mM Tris pH 7.2, 10 mM disaccharide

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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: Jun 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32930 / % possible obs: 94.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 24.27 Å2 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.054 / Rrim(I) all: 0.142 / Χ2: 2.235 / Net I/av σ(I): 23.038 / Net I/σ(I): 7.7 / Num. measured all: 225197
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.035.30.513510.8810.2240.5511.0178
2.03-2.076.10.46513420.9320.1930.5051.01679.3
2.07-2.116.20.41314310.940.170.4481.10382.3
2.11-2.156.30.4214480.9270.1740.4561.16183.4
2.15-2.26.40.38315010.9690.1560.4141.2186.8
2.2-2.256.50.33315270.9660.1350.361.36890.1
2.25-2.316.60.34516510.9530.1410.3741.32695.1
2.31-2.376.80.33317190.9710.1350.3591.37598.7
2.37-2.447.20.34517030.9760.1380.3721.40999.7
2.44-2.527.40.31317170.9780.1230.3361.568100
2.52-2.617.50.29117580.9780.1140.3131.608100
2.61-2.717.50.23617260.9850.0920.2531.875100
2.71-2.847.40.19517300.9910.0770.212.134100
2.84-2.997.40.16817260.9910.0670.1812.463100
2.99-3.177.20.13717670.9930.0550.1482.969100
3.17-3.4270.11717290.9920.0480.1263.441100
3.42-3.766.90.117580.9940.0420.1093.874100
3.76-4.316.70.08517700.9950.0360.0924.276100
4.31-5.436.80.0717490.9960.0290.0763.9499.7
5.43-506.60.06418270.9960.0260.0693.70999.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementResolution: 2→28.229 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 1643 5 %
Rwork0.1979 31221 -
obs0.2001 32864 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.96 Å2 / Biso mean: 35.55 Å2 / Biso min: 13.24 Å2
Refinement stepCycle: final / Resolution: 2→28.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 54 346 3428
Biso mean--40.24 38.88 -
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0263270
X-RAY DIFFRACTIONf_angle_d0.9794427
X-RAY DIFFRACTIONf_chiral_restr0.042526
X-RAY DIFFRACTIONf_plane_restr0.005586
X-RAY DIFFRACTIONf_dihedral_angle_d11.8641205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9973-2.0560.33961090.26632076218576
2.056-2.12240.28221180.24692237235582
2.1224-2.19820.2761090.23682345245486
2.1982-2.28620.33361230.23512518264192
2.2862-2.39020.27921490.2322697284699
2.3902-2.51610.28271370.224827312868100
2.5161-2.67360.29241570.232127572914100
2.6736-2.87990.26491560.225227162872100
2.8799-3.16940.25611360.214927822918100
3.1694-3.62720.24981500.192427702920100
3.6272-4.56670.18341440.161327722916100
4.5667-28.23210.19441550.15632820297599

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