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- PDB-6tzl: The structure of the Streptococcus gordonii surface protein SspB ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tzl | ||||||
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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 | ||||||
![]() | Surface protein adhesin | ||||||
![]() | CELL ADHESION / Streptococcus mutans / AgI/II / spaP (variable domain) | ||||||
Function / homology | ![]() endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / ER to Golgi transport vesicle membrane / membrane fusion / extracellular region / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schormann, N. / Deivanayagam, C. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 639.7 KB | Display | ![]() |
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PDB format | ![]() | 525.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 293.2 KB | Display | ![]() |
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Full document | ![]() | 293.1 KB | Display | |
Data in XML | ![]() | 1.1 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6q2kC ![]() 6q2lC ![]() 6ubvC ![]() 3ipkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 46717.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 4000, 650mM lithium sulfate, 50mM Tris, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.46 Å2 / Biso mean: 24.105 Å2 / Biso min: 11.34 Å2
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Refinement step | Cycle: final / Resolution: 1.6→34.96 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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