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- PDB-6ubv: The structure of the Streptococcus gordonii surface protein SspB ... -

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Basic information

Entry
Database: PDB / ID: 6ubv
TitleThe structure of the Streptococcus gordonii surface protein SspB in complex with TEV peptide provides clues to the adherence of oral streptococcal adherence to salivary agglutinin
ComponentsSurface protein adhesin
KeywordsCELL ADHESION / Streptococcus mutans / AgI/II / spaP (variable domain)
Function / homology
Function and homology information


protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / extracellular region / metal ion binding / identical protein binding / membrane
Similarity search - Function
Major cell-surface adhesin PAc / Major cell-surface adhesin PAc / Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Antigen I/II, N-terminal / Adhesin P1 N-terminal domain / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C ...Major cell-surface adhesin PAc / Major cell-surface adhesin PAc / Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Antigen I/II, N-terminal / Adhesin P1 N-terminal domain / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Cross-wall-targeting lipoprotein motif / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-SNZ / Surface protein adhesin / Major cell-surface adhesin PAc
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchormann, N. / Deivanayagam, C.
CitationJournal: To Be Published
Title: The structure of the Streptococcus gordonii surface protein SspB in complex with TEV peptide provides clues to the adherence of oral streptococcal adherence to salivary agglutinin
Authors: Schormann, N. / Deivanayagam, C.
History
DepositionSep 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface protein adhesin
B: Surface protein adhesin
C: Surface protein adhesin
D: Surface protein adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,69720
Polymers186,8724
Non-polymers1,82516
Water6,846380
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.810, 132.697, 243.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 457 through 843)
21(chain B and (resid 457 through 459 or (resid 460...
31(chain C and (resid 457 through 459 or (resid 460...
41(chain D and (resid 457 through 459 or (resid 460...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNTHRTHR(chain A and resid 457 through 843)AA457 - 84325 - 411
21GLNGLNASPASP(chain B and (resid 457 through 459 or (resid 460...BB457 - 45925 - 27
22LEULEUALAALA(chain B and (resid 457 through 459 or (resid 460...BB460 - 46128 - 29
23GLUGLUTHRTHR(chain B and (resid 457 through 459 or (resid 460...BB450 - 84318 - 411
24GLUGLUTHRTHR(chain B and (resid 457 through 459 or (resid 460...BB450 - 84318 - 411
25GLUGLUTHRTHR(chain B and (resid 457 through 459 or (resid 460...BB450 - 84318 - 411
26GLUGLUTHRTHR(chain B and (resid 457 through 459 or (resid 460...BB450 - 84318 - 411
31GLNGLNASPASP(chain C and (resid 457 through 459 or (resid 460...CC457 - 45925 - 27
32LEULEUALAALA(chain C and (resid 457 through 459 or (resid 460...CC460 - 46128 - 29
33ALAALAPROPRO(chain C and (resid 457 through 459 or (resid 460...CC447 - 84515 - 413
34ALAALAPROPRO(chain C and (resid 457 through 459 or (resid 460...CC447 - 84515 - 413
35ALAALAPROPRO(chain C and (resid 457 through 459 or (resid 460...CC447 - 84515 - 413
36ALAALAPROPRO(chain C and (resid 457 through 459 or (resid 460...CC447 - 84515 - 413
41GLNGLNASPASP(chain D and (resid 457 through 459 or (resid 460...DD457 - 45925 - 27
42LEULEUALAALA(chain D and (resid 457 through 459 or (resid 460...DD460 - 46128 - 29
43GLNGLNALAALA(chain D and (resid 457 through 459 or (resid 460...DD457 - 84425 - 412
44GLNGLNALAALA(chain D and (resid 457 through 459 or (resid 460...DD457 - 84425 - 412
45GLNGLNALAALA(chain D and (resid 457 through 459 or (resid 460...DD457 - 84425 - 412
46GLNGLNALAALA(chain D and (resid 457 through 459 or (resid 460...DD457 - 84425 - 412

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Surface protein adhesin


Mass: 46717.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: spaP / Plasmid: pET23-d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9E3B4, UniProt: P11657*PLUS

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Non-polymers , 6 types, 396 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SNZ / N-(3,4-dihydroxyphenyl)-N'-[2-(3,4-dihydroxyphenyl)ethyl]urea


Mass: 304.298 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H16N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 4000, 650 mM lithium sulfate, 50 mM Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 5, 2016 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→29.725 Å / Num. obs: 56119 / % possible obs: 94 % / Redundancy: 4.2 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.058 / Rrim(I) all: 0.123 / Net I/σ(I): 11.6
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 2 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3400 / CC1/2: 0.816 / Rpim(I) all: 0.321 / Rrim(I) all: 0.53 / % possible all: 71.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
DIALS1.10.0data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TZL

6tzl


Resolution: 2.7→29.72 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.78
RfactorNum. reflection% reflection
Rfree0.2497 2738 4.89 %
Rwork0.2065 --
obs0.2086 56040 93.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.79 Å2 / Biso mean: 26.2718 Å2 / Biso min: 6.05 Å2
Refinement stepCycle: final / Resolution: 2.7→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12122 0 117 380 12619
Biso mean--51.07 21.1 -
Num. residues----1573
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4648X-RAY DIFFRACTION3.18TORSIONAL
12B4648X-RAY DIFFRACTION3.18TORSIONAL
13C4648X-RAY DIFFRACTION3.18TORSIONAL
14D4648X-RAY DIFFRACTION3.18TORSIONAL
LS refinement shellResolution: 2.7→2.7465 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3188 117 -
Rwork0.2537 1897 -
obs--68 %

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