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Yorodumi- PDB-5hbb: Crystal structure of shaft pilin spaA from Lactobacillus rhamnosu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hbb | ||||||
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Title | Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - E139A mutant | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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 | 5hbb.cif.gz | 319.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hbb.ent.gz | 259.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/5hbb ftp://data.pdbj.org/pub/pdb/validation_reports/hb/5hbb | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) 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: Chemical | ChemComp-NA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.03 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
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: 0.95372 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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