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Yorodumi- PDB-5f44: Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f44 | ||||||
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Title | Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG | ||||||
Components | Cell surface protein SpaA | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 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 | 5f44.cif.gz | 325.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f44.ent.gz | 264.3 KB | Display | PDB format |
PDBx/mmJSON format | 5f44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f44_validation.pdf.gz | 456.3 KB | Display | wwPDB validaton report |
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Full document | 5f44_full_validation.pdf.gz | 458.6 KB | Display | |
Data in XML | 5f44_validation.xml.gz | 36.7 KB | Display | |
Data in CIF | 5f44_validation.cif.gz | 55.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/5f44 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/5f44 | HTTPS FTP |
-Related structure data
Related structure data | 5faaC 5fgrC 5fgsC 5fieC 5hbbC 5hdlC 5htsC 5j4mC 3phsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30723.498 Da / Num. of mol.: 3 / Fragment: UNP residues 35-302 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.32 Å3/Da / Density % sol: 71.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.35 M trisodium citrate, 14% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2012 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.904→31.16 Å / Num. obs: 105419 / % possible obs: 90 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.91 |
Reflection shell | Resolution: 1.904→1.972 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.14 / % possible all: 63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PHS Resolution: 1.904→31.156 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.39 / 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: 1.904→31.156 Å
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Refine LS restraints |
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LS refinement shell |
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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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