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- PDB-5hbb: Crystal structure of shaft pilin spaA from Lactobacillus rhamnosu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hbb | ||||||
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Title | Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - E139A mutant | ||||||
![]() | Cell surface protein SpaA![]() | ||||||
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Function / homology | ![]() Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / ![]() ![]() ![]() ![]() ![]() Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit Authors: Chaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / 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 | ![]() | 319.5 KB | Display | ![]() |
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PDB format | ![]() | 259.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5f44SC ![]() 5faaC ![]() 5fgrC ![]() 5fgsC ![]() 5fieC ![]() 5hdlC ![]() 5htsC ![]() 5j4mC 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0
NCS ensembles :
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Components
#1: Protein | ![]() Mass: 30665.463 Da / Num. of mol.: 3 / Fragment: UNP residues 35-302 / Mutation: E139A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-NA / #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.49 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium thiocynate, 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2015 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.47→111.8 Å / Num. obs: 44441 / % possible obs: 83.53 % / Redundancy: 5 % / Rmerge(I) obs: 0.08946 / Rsym value: 0.09943 / Net I/σ(I): 17.36 |
Reflection shell | Resolution: 2.466→2.554 Å / Redundancy: 4 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.84 / % possible all: 27.02 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5F44 Resolution: 2.47→111.8 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.887 / SU B: 13.007 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.418 Å2
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Refinement step | Cycle: 1 / Resolution: 2.47→111.8 Å
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Refine LS restraints |
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