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- PDB-6yro: Streptococcus suis SadP mutant - N285D -

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Basic information

Entry
Database: PDB / ID: 6yro
TitleStreptococcus suis SadP mutant - N285D
ComponentsSadP
KeywordsSUGAR BINDING PROTEIN / Bacterial adhesion / glycoconjugates / Streptococcus suis / galabiose / adhesins
Function / homologyLPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / translation initiation factor activity / membrane / SadP
Function and homology information
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPapageorgiou, A.C. / Haataja, S.
Citation
Journal: J.Biol.Chem. / Year: 2020
Title: The binding mechanism of the virulence factor Streptococcus suis adhesin P subtype to globotetraosylceramide is associated with systemic disease.
Authors: Madar Johansson, M. / Belurier, E. / Papageorgiou, A.C. / Sundin, A.P. / Rahkila, J. / Kallonen, T. / Nilsson, U.J. / Maatsola, S. / Nyholm, T.K.M. / Kapyla, J. / Corander, J. / Leino, R. / ...Authors: Madar Johansson, M. / Belurier, E. / Papageorgiou, A.C. / Sundin, A.P. / Rahkila, J. / Kallonen, T. / Nilsson, U.J. / Maatsola, S. / Nyholm, T.K.M. / Kapyla, J. / Corander, J. / Leino, R. / Finne, J. / Teneberg, S. / Haataja, S.
#1: Journal: Chemistry / Year: 2018
Title: Rationally Designed Chemically Modified Glycodendrimer Inhibits Streptococcus suis Adhesin SadP at Picomolar Concentrations.
Authors: Haataja, S. / Verma, P. / Fu, O. / Papageorgiou, A.C. / Poysti, S. / Pieters, R.J. / Nilsson, U.J. / Finne, J.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_a6 ..._atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_a6 / _atom_type.pdbx_scat_Cromer_Mann_b5 / _atom_type.pdbx_scat_Cromer_Mann_b6 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: SadP
A: SadP
B: SadP
C: SadP
E: SadP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,48315
Polymers126,7705
Non-polymers71410
Water16,322906
1
D: SadP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5383
Polymers25,3541
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SadP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5614
Polymers25,3541
Non-polymers2073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: SadP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5383
Polymers25,3541
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: SadP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4693
Polymers25,3541
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: SadP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3772
Polymers25,3541
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.132, 80.799, 130.740
Angle α, β, γ (deg.)90.000, 113.133, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
SadP


Mass: 25353.961 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Gene: sadP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5DSS1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#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


Mass: 18.015 Da / Num. of mol.: 906 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 49.1 % / Description: Thin rods
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.3-1.5 M sodium citrate tribasic, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→66.3 Å / Num. obs: 71993 / % possible obs: 94.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.47 Å2 / CC1/2: 0.989 / Rrim(I) all: 0.163 / Net I/σ(I): 6.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3213 / CC1/2: 0.591 / Rrim(I) all: 0.717 / % possible all: 69

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHASERphasing
XDSdata processing
Aimlessdata scaling
Aimlessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bob

5bob


Resolution: 2.05→45.68 Å / SU ML: 0.2381 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1712 2.38 %RANDOM
Rwork0.1738 70223 --
obs0.175 71935 94.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.22 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8175 0 45 906 9126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818398
X-RAY DIFFRACTIONf_angle_d0.932411376
X-RAY DIFFRACTIONf_chiral_restr0.05331247
X-RAY DIFFRACTIONf_plane_restr0.00491474
X-RAY DIFFRACTIONf_dihedral_angle_d8.0231100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.33861040.25494285X-RAY DIFFRACTION69.76
2.11-2.180.27511190.24244878X-RAY DIFFRACTION79.28
2.18-2.260.30251370.22715609X-RAY DIFFRACTION91.11
2.26-2.350.28241490.21126077X-RAY DIFFRACTION99.27
2.35-2.450.26761480.20816113X-RAY DIFFRACTION99.49
2.45-2.580.26831500.2026144X-RAY DIFFRACTION99.49
2.58-2.740.28551490.20376112X-RAY DIFFRACTION99.73
2.74-2.960.2311510.19496169X-RAY DIFFRACTION99.94
2.96-3.250.21341510.17146192X-RAY DIFFRACTION99.89
3.25-3.720.20021500.14666170X-RAY DIFFRACTION99.83
3.72-4.690.17421510.13036200X-RAY DIFFRACTION99.78
4.69-45.680.1811530.1616274X-RAY DIFFRACTION99.38

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