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Yorodumi- PDB-5fie: Crystal structure of N-terminal domain of shaft pilin spaA from L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fie | ||||||
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Title | Crystal structure of N-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus GG | ||||||
Components | Cell surface protein SpaACell membrane | ||||||
Keywords | CELL ADHESION / Pilin / spaA / probiotic / isopeptide / SpaCBA pili / adhesin | ||||||
Function / homology | Function and homology information 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Lactobacillus rhamnosus GG (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V. | ||||||
Funding support | India, 1items
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Citation | Journal: Sci Rep / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fie.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fie.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/5fie ftp://data.pdbj.org/pub/pdb/validation_reports/fi/5fie | HTTPS FTP |
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-Related structure data
Related structure data | 5f44SC 5faaC 5fgrC 5fgsC 5hbbC 5hdlC 5htsC 5j4mC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16716.312 Da / Num. of mol.: 1 / Fragment: UNP residues 35-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / Strain: GG / Gene: LRHM_0426 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: C7T9P4 |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.21 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium formate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.89 Å / Num. obs: 13657 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.19 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 3.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F44 Resolution: 2→44.307 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→44.307 Å
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Refine LS restraints |
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LS refinement shell |
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