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

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Basic information

Entry
Database: PDB / ID: 6tzl
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
Surface protein adhesin / Major cell-surface adhesin PAc
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 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)187,44810
Polymers186,8724
Non-polymers5766
Water34,4811914
1
B: Surface protein adhesin
C: Surface protein adhesin
D: Surface protein adhesin
hetero molecules

A: Surface protein adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,44810
Polymers186,8724
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area6140 Å2
ΔGint-94 kcal/mol
Surface area66270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.965, 133.331, 246.072
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
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYSAA459 - 84127 - 409
21ASPASPLYSLYSBB459 - 84127 - 409
12TYRTYRPROPROAA456 - 84224 - 410
22TYRTYRPROPROCC456 - 84224 - 410
13TYRTYRPROPROAA456 - 84224 - 410
23TYRTYRPROPRODD456 - 84224 - 410
14ASPASPLYSLYSBB459 - 84127 - 409
24ASPASPLYSLYSCC459 - 84127 - 409
15ASPASPLYSLYSBB459 - 84127 - 409
25ASPASPLYSLYSDD459 - 84127 - 409
16ALAALAALAALACC447 - 84415 - 412
26ALAALAALAALADD447 - 84415 - 412

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#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: pET-23d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9E3B4, UniProt: P11657*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1914 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 4000, 650mM lithium sulfate, 50mM Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 285302 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.056 / Χ2: 0.912 / Net I/av σ(I): 24.3 / Net I/σ(I): 8.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 14076 / Χ2: 0.708 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IPK

3ipk


Resolution: 1.6→34.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.064 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 14429 5.1 %RANDOM
Rwork0.1796 ---
obs0.1803 270668 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.46 Å2 / Biso mean: 24.105 Å2 / Biso min: 11.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å2-0 Å2
2---1.95 Å20 Å2
3---1.22 Å2
Refinement stepCycle: final / Resolution: 1.6→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12163 0 30 1914 14107
Biso mean--70.81 36.12 -
Num. residues----1575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01312559
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711267
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.64417042
X-RAY DIFFRACTIONr_angle_other_deg1.3881.58526455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02951601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35525.94564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.197152168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.7681517
X-RAY DIFFRACTIONr_chiral_restr0.0610.21647
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022348
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A126460.07
12B126460.07
21A125680.09
22C125680.09
31A125980.08
32D125980.08
41B124450.09
42C124450.09
51B124770.08
52D124770.08
61C129410.07
62D129410.07
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 1053 -
Rwork0.268 19654 -
all-20707 -
obs--99.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2390.01150.0310.2243-0.14970.3028-0.0670.0457-0.063-0.00960.0328-0.0066-0.04790.01320.03420.0801-0.0184-0.00290.0201-0.01750.0584-8.19120.8227-28.6363
20.5153-0.3222-0.05380.32720.13450.0944-0.04730.04780.02780.03610.00340.01440.00540.01260.04380.06210.00450.01810.02-0.00630.0726-0.5488-43.1697-27.6892
30.02530.0208-0.05060.45040.12920.19410.01820.01020.00250.0017-0.0099-0.02540.0026-0.0343-0.00830.06990.0002-0.00870.026-0.00660.073518.7216-74.9894-24.1266
40.38140.3789-0.08510.4649-0.15650.078-0.03040.05720.0202-0.00440.05560.0534-0.0134-0.0101-0.02530.0504-0.0197-0.00780.01610.02220.1031-27.04-100.4236-28.2568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A456 - 517
2X-RAY DIFFRACTION1A518 - 611
3X-RAY DIFFRACTION1A612 - 679
4X-RAY DIFFRACTION1A680 - 843
5X-RAY DIFFRACTION2B459 - 494
6X-RAY DIFFRACTION2B495 - 517
7X-RAY DIFFRACTION2B518 - 611
8X-RAY DIFFRACTION2B612 - 679
9X-RAY DIFFRACTION2B680 - 842
10X-RAY DIFFRACTION3C444 - 517
11X-RAY DIFFRACTION3C518 - 611
12X-RAY DIFFRACTION3C612 - 668
13X-RAY DIFFRACTION3C669 - 847
14X-RAY DIFFRACTION4D447 - 517
15X-RAY DIFFRACTION4D518 - 611
16X-RAY DIFFRACTION4D612 - 668
17X-RAY DIFFRACTION4D669 - 690
18X-RAY DIFFRACTION4D691 - 780
19X-RAY DIFFRACTION4D781 - 845

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