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- PDB-9q5e: Hsa bound to Neu5Ac alpha2,3 Gal beta OMe -

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Basic information

Entry
Database: PDB / ID: 9q5e
TitleHsa bound to Neu5Ac alpha2,3 Gal beta OMe
ComponentsStreptococcal hemagglutinin
KeywordsSUGAR BINDING PROTEIN / Glycan binding protein
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: 1.29 Å
AuthorsIverson, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Hsa bound to Neu5Ac alpha2,3 Gal beta OMe
Authors: Iverson, T.M.
History
DepositionAug 20, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionNov 26, 2025ID: 8ST5
Revision 1.0Nov 26, 2025Provider: 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)23,6414
Polymers23,0921
Non-polymers5493
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.302, 57.567, 75.685
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: 23092.367 Da / Num. of mol.: 1 / Mutation: D381E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus (bacteria) / Gene: hsa, SGO_0966 / Production host: Escherichia coli (E. coli) / References: UniProt: A8AWU7
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-methyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 485.437 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DNeup5Aca2-3DGalp[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OC][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.44 %
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 Neu5Ac 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: 0.97946 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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.29→38.87 Å / Num. obs: 45264 / % possible obs: 91.3 % / Redundancy: 11 % / Biso Wilson estimate: 17.17 Å2 / CC1/2: 1 / Rpim(I) all: 0.023 / Rsym value: 0.079 / Net I/σ(I): 115.4
Reflection shellResolution: 1.29→1.31 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 45264 / CC1/2: 0.963 / Rpim(I) all: 0.216 / Rsym value: 0.465

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→38.87 Å / SU ML: 0.1413 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.1444
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.191 3017 6.67 %
Rwork0.1606 42247 -
obs0.1626 45264 90.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.25 Å2
Refinement stepCycle: LAST / Resolution: 1.29→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 35 304 1925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451713
X-RAY DIFFRACTIONf_angle_d0.77882358
X-RAY DIFFRACTIONf_chiral_restr0.0697272
X-RAY DIFFRACTIONf_plane_restr0.0098317
X-RAY DIFFRACTIONf_dihedral_angle_d12.2106635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.310.3893590.327802X-RAY DIFFRACTION38.3
1.31-1.340.3439760.27381099X-RAY DIFFRACTION52.13
1.34-1.360.2986950.22951358X-RAY DIFFRACTION65.01
1.36-1.380.27111120.18491558X-RAY DIFFRACTION73.89
1.38-1.410.23871190.16891703X-RAY DIFFRACTION81.45
1.41-1.440.20811360.15871908X-RAY DIFFRACTION90.56
1.44-1.470.20841430.16072005X-RAY DIFFRACTION95.64
1.47-1.50.20441440.16152060X-RAY DIFFRACTION98.61
1.5-1.540.21131500.16092095X-RAY DIFFRACTION99.07
1.54-1.580.2041510.16132077X-RAY DIFFRACTION98.58
1.58-1.630.24561480.16982097X-RAY DIFFRACTION99.2
1.63-1.680.20941500.16322079X-RAY DIFFRACTION98.41
1.68-1.740.21051510.14942109X-RAY DIFFRACTION99.12
1.74-1.810.19411500.15182099X-RAY DIFFRACTION99.29
1.81-1.890.20831500.1532096X-RAY DIFFRACTION99.2
1.89-1.990.17911510.15212122X-RAY DIFFRACTION99.26
1.99-2.120.21261490.14852114X-RAY DIFFRACTION99.65
2.12-2.280.15511560.14032138X-RAY DIFFRACTION99.48
2.28-2.510.17241540.15322154X-RAY DIFFRACTION99.44
2.51-2.880.19851540.16662141X-RAY DIFFRACTION99.44
2.88-3.620.1691540.15732168X-RAY DIFFRACTION98.89
3.62-38.870.18661650.16992265X-RAY DIFFRACTION98.5

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