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- PDB-6q2k: The structure of the Streptococcus gordonii surface protein SspB ... -

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Basic information

Entry
Database: PDB / ID: 6q2k
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 / Resolution: 2 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)37,4972
Polymers37,4571
Non-polymers401
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.505, 121.505, 50.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-902-

HOH

21A-1048-

HOH

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Components

#1: Protein Agglutinin receptor / SSP-5


Mass: 37457.270 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3M Sodium acetate trihydrate, 0.1M Hepes, pH 7.0

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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: Mar 10, 2014 / 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: 2→30 Å / Num. obs: 25664 / % possible obs: 97.7 % / Redundancy: 15.5 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.027 / Rrim(I) all: 0.122 / Χ2: 1.056 / Net I/av σ(I): 20.1 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1071 / CC1/2: 0.839 / Rpim(I) all: 0.275 / Rrim(I) all: 0.527 / Χ2: 1.027 / % possible all: 82.8

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Processing

Software
NameVersionClassification
HKL-20002.3.8data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
HKL-20002.3.8data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wd6

2wd6


Resolution: 2→29.47 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.291 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.163
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 1303 5.1 %RANDOM
Rwork0.1935 ---
obs0.1955 24276 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.58 Å2 / Biso mean: 31.4 Å2 / Biso min: 16.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 1 281 2752
Biso mean--49.18 39.79 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022524
X-RAY DIFFRACTIONr_bond_other_d0.0020.022221
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9333419
X-RAY DIFFRACTIONr_angle_other_deg0.83735192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90825.47117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6915417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.219157
X-RAY DIFFRACTIONr_chiral_restr0.0650.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.326 79 5.2 %
Rwork0.269 1529 -
obs--84.77 %

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