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- PDB-6q2l: The structure of the Streptococcus gordonii surface protein SspB ... -

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Basic information

Entry
Database: PDB / ID: 6q2l
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
ComponentsAgglutinin receptor
KeywordsCELL ADHESION / SspB / variable domain
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / 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 / Antigen I/II, N-terminal ...Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / 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 / Antigen I/II, N-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / Adhesin P1 N-terminal domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agglutinin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0863
Polymers35,9701
Non-polymers1162
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.223, 47.695, 64.652
Angle α, β, γ (deg.)90.000, 113.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Agglutinin receptor / SSP-5


Mass: 35969.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Gene: ssp5, sspB / Plasmid: pET23d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16952
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-25% PEG 8000, 0.1M succinic acid, pH 5.0-5.5, 100mM MgCl2
PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 30, 2017 / Details: Osmic Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 31075 / % possible obs: 98.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.047 / Rrim(I) all: 0.097 / Χ2: 2.661 / Net I/av σ(I): 19.1 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1321 / CC1/2: 0.714 / Rpim(I) all: 0.38 / Rrim(I) all: 0.567 / Χ2: 1.409 / % possible all: 83.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.53 Å37.15 Å
Translation5.53 Å37.15 Å

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Processing

Software
NameVersionClassification
HKL-20002.3.8data scaling
PHASER2.7.17phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
HKL-20002.3.8data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q2K

6q2k


Resolution: 1.8→37.15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.094 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1554 5 %RANDOM
Rwork0.195 ---
obs0.197 29507 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.66 Å2 / Biso mean: 22.5 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.02 Å2
2---0.08 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.8→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 7 351 2703
Biso mean--19.21 32.05 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022436
X-RAY DIFFRACTIONr_bond_other_d0.0020.022138
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9313297
X-RAY DIFFRACTIONr_angle_other_deg0.88235003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7625306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39625.487113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41515407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.989157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.302 147 5.5 %
Rwork0.303 2674 -
obs--90.59 %
Refinement TLS params.Method: refined / Origin x: -14.821 Å / Origin y: 3.2163 Å / Origin z: -4.0907 Å
111213212223313233
T0.0057 Å2-0.0019 Å2-0.0077 Å2-0.0313 Å20.0105 Å2--0.0164 Å2
L0.4868 °2-0.1449 °20.0698 °2-0.5505 °2-0.018 °2--0.2105 °2
S0.0015 Å °-0.0807 Å °0.0024 Å °-0.0497 Å °0.0288 Å °0.0512 Å °0.0127 Å °-0.0097 Å °-0.0302 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A462 - 478
2X-RAY DIFFRACTION1A479 - 514
3X-RAY DIFFRACTION1A515 - 547
4X-RAY DIFFRACTION1A548 - 642
5X-RAY DIFFRACTION1A643 - 738
6X-RAY DIFFRACTION1A739 - 762

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