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- PDB-8st5: Streptococcus gordonii str. Challis Hsa bound to Neu5Ac -

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Basic information

Entry
Database: PDB / ID: 8st5
TitleStreptococcus gordonii str. Challis Hsa bound to Neu5Ac
ComponentsStreptococcal hemagglutinin
KeywordsPROTEIN BINDING / Bacterial / Adhesin / Glycan binding
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMorrison, K.M.A. / Iverson, T.M.
Funding support United States, 4items
OrganizationGrant numberCountry
Department of Veterans Affairs (VA, United States)RO1AI106987 United States
Department of Veterans Affairs (VA, United States)GM137458 United States
American Heart Association14GRNT20390021 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM007628 United States
CitationJournal: To Be Published
Title: Hsa Siglec +Unique Domains bound to Neu5Ac alpha2, 3 Gal
Authors: Morrison, K.M.A. / Iverson, T.M.
History
DepositionMay 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptococcal hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3333
Polymers25,8381
Non-polymers4942
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.067, 57.695, 75.952
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: 25838.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus (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


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 276 / 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: 1.91 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 1 uL protein (21.6 mg/ml in 20 mM Tris-HCl, pH 7.2) and 2 uL reservoir solution over 50 uL of reservoir solution (0.1 M Succinate/Phosphate/Glycine pH 10.0 and 25% PEG 3350). Fully formed ...Details: 1 uL protein (21.6 mg/ml in 20 mM Tris-HCl, pH 7.2) and 2 uL reservoir solution over 50 uL of reservoir solution (0.1 M Succinate/Phosphate/Glycine pH 10.0 and 25% PEG 3350). Fully formed crystals were soaked in reservoir solution supple-mented with 5 mM Neu5Gc alpha2,3GalOMe

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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 PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 33040 / % possible obs: 90.4 % / Redundancy: 11.3 % / Biso Wilson estimate: 17.19 Å2 / CC1/2: 1 / Net I/σ(I): 37.97
Reflection shellResolution: 1.45→1.48 Å / Num. unique obs: 2592 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-20001.20_4459data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→39.39 Å / SU ML: 0.1431 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.5737
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1989 1655 5.01 %
Rwork0.1653 31385 -
obs0.1669 33040 89.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.96 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 33 276 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931680
X-RAY DIFFRACTIONf_angle_d1.08562305
X-RAY DIFFRACTIONf_chiral_restr0.0907265
X-RAY DIFFRACTIONf_plane_restr0.013308
X-RAY DIFFRACTIONf_dihedral_angle_d13.1315624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.3083750.22881335X-RAY DIFFRACTION46.61
1.49-1.540.24781010.21111754X-RAY DIFFRACTION61.87
1.54-1.590.25621130.19852276X-RAY DIFFRACTION79.24
1.59-1.660.26211360.20082755X-RAY DIFFRACTION95.54
1.66-1.730.2631520.17322813X-RAY DIFFRACTION98.21
1.73-1.820.20091500.15592827X-RAY DIFFRACTION98.74
1.82-1.940.20151500.15532892X-RAY DIFFRACTION99.48
1.94-2.090.22041540.15352880X-RAY DIFFRACTION99.84
2.09-2.30.19871530.14682915X-RAY DIFFRACTION99.61
2.3-2.630.19191520.16022910X-RAY DIFFRACTION99.58
2.63-3.320.20251560.17082954X-RAY DIFFRACTION99.65
3.32-39.390.17051630.16443074X-RAY DIFFRACTION99.6

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