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- PDB-8st6: Hsa Siglec + Unique domains bound to Neu5Gc alpha2,3 Gal beta OMe -

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Basic information

Entry
Database: PDB / ID: 8st6
TitleHsa Siglec + Unique domains bound to Neu5Gc alpha2,3 Gal beta OMe
ComponentsStreptococcal hemagglutinin
KeywordsSUGAR BINDING PROTEIN / adhesin / streptococcus / sialoglycan
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 substr. CH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsStubbs, H.E. / Iverson, T.M.
Funding support United States, 4items
OrganizationGrant numberCountry
Department of Veterans Affairs (VA, United States)R01AI130684 United States
Department of Veterans Affairs (VA, United States)R01AI106987 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137458 United States
American Heart Association14GRNT20390021 United States
CitationJournal: To Be Published
Title: Hsa Siglec + Unique domains bound to Neu5Gc alpha2,3 Gal beta OMe
Authors: Stubbs, H.E. / 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

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Assembly

Deposited unit
A: Streptococcal hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3854
Polymers25,8371
Non-polymers5473
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


Mass: 25837.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii str. Challis substr. CH1 (bacteria)
Strain: Challis / Gene: hsa / Variant: substr. DL1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A8AWU7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-USR / methyl 3-O-[3,5-dideoxy-5-(2-hydroxyacetamido)-L-glycero-alpha-D-gulo-non-2-ulopyranonosyl]-beta-D-talopyranoside


Mass: 501.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C18H31NO15 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / 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: 1.96 Å3/Da / Density % sol: 37.1 %
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: 1.3→50 Å / Num. obs: 45613 / % possible obs: 91.3 % / Redundancy: 11 % / Biso Wilson estimate: 17.19 Å2 / CC1/2: 1 / Net I/σ(I): 48.1
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1140 / CC1/2: 0.963

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EFC

6efc


Resolution: 1.45→39.39 Å / SU ML: 0.1557 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.5294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2081 1655 5.01 %
Rwork0.171 31385 -
obs0.1728 33040 89.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.18 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 36 276 1888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621663
X-RAY DIFFRACTIONf_angle_d1.39942281
X-RAY DIFFRACTIONf_chiral_restr0.1353266
X-RAY DIFFRACTIONf_plane_restr0.0116302
X-RAY DIFFRACTIONf_dihedral_angle_d13.9547597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.3397750.2471335X-RAY DIFFRACTION46.61
1.49-1.540.26361010.22991754X-RAY DIFFRACTION61.87
1.54-1.590.25191130.21682276X-RAY DIFFRACTION79.24
1.59-1.660.29921360.21592755X-RAY DIFFRACTION95.54
1.66-1.730.24241520.18472813X-RAY DIFFRACTION98.21
1.73-1.820.21151500.16852827X-RAY DIFFRACTION98.74
1.82-1.940.20091500.16182892X-RAY DIFFRACTION99.48
1.94-2.090.23361540.15782880X-RAY DIFFRACTION99.84
2.09-2.30.18931530.15062915X-RAY DIFFRACTION99.58
2.3-2.630.19811520.16562910X-RAY DIFFRACTION99.58
2.63-3.320.21241560.1752954X-RAY DIFFRACTION99.65
3.32-39.390.18711630.16723074X-RAY DIFFRACTION99.6

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