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- PDB-7bvx: Crystal structure of C-terminal fragment of pilus adhesin SpaC fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bvx | ||||||
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Title | Crystal structure of C-terminal fragment of pilus adhesin SpaC from Lactobacillus rhamnosus GG-Iodide soaked | ||||||
![]() | Pilus assembly protein | ||||||
![]() | CELL ADHESION / Pilus adhesin / Tip pilin / SpaCBA pilus / sortase / Lactobacillus rhamnosus GG / pili / fimbria / Probiotics / SpaC / surface protein | ||||||
Function / homology | ![]() Prealbumin-like fold domain / Prealbumin-like fold domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kant, A. / Palva, A. / von Ossowski, I. / Krishnan, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of lactobacillar SpaC reveals an atypical five-domain pilus tip adhesin: Exposing its substrate-binding and assembly in SpaCBA pili. Authors: Kant, A. / Palva, A. / von Ossowski, I. / Krishnan, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6m3ySC ![]() 6m48C ![]() 6m7cC 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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Components
#1: Protein | Mass: 31517.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MGSSHHHHHHSSGLVPRGSHMTNQQYGFQFQKKTTDGTDLSADQLKAMQFNLTQYSDNSF QQASKTNAITSTDLQALAPGYYGIQEAAAPTGYQLDGTTYLFQLTSDGQWQYHGTKDNVT SGSVINGQQTLNPVGDKSDDFTVTGDHQQILTLTKYDEPKPSMTLRVIKQDNQSQYLAGA ...Details: MGSSHHHHHHSSGLVPRGSHMTNQQYGFQFQKKTTDGTDLSADQLKAMQFNLTQYSDNSF QQASKTNAITSTDLQALAPGYYGIQEAAAPTGYQLDGTTYLFQLTSDGQWQYHGTKDNVT SGSVINGQQTLNPVGDKSDDFTVTGDHQQILTLTKYDEPKPSMTLRVIKQDNQSQYLAGA AFTLQPSAGEAETITSSATSEGQAFATKLVADGTYTMSETKAPDGYQSNPAKIAIQVATT GKEATVTIDGEALKPGESKNGYTLAIDGSTITLQAINQPLAILPLEHHHHHH Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-IOD / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 65.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / Details: 2M Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4231 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→57.53 Å / Num. obs: 6345 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.016 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 3.35→3.41 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 324 / CC1/2: 0.88 / Rpim(I) all: 0.24 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6M3Y Resolution: 3.36→57.46 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.856 / SU B: 44.209 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.624 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 145.844 Å2
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Refinement step | Cycle: 1 / Resolution: 3.36→57.46 Å
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Refine LS restraints |
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