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Yorodumi- PDB-5fgr: Crystal structure of C-terminal domain of shaft pilin spaA from L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fgr | ||||||
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Title | Crystal structure of C-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus GG - P21212 space group with Yb Heavy atom | ||||||
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 / SAD / Resolution: 2.79 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 | 5fgr.cif.gz | 194.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fgr.ent.gz | 163.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/5fgr ftp://data.pdbj.org/pub/pdb/validation_reports/fg/5fgr | HTTPS FTP |
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-Related structure data
Related structure data | 5f44C 5faaC 5fgsC 5fieC 5hbbC 5hdlC 5htsC 5j4mC 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 14575.775 Da / Num. of mol.: 4 / Fragment: C-terminal domain, residues 177-302 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 | ChemComp-YB / #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: 2.34 Å3/Da / Density % sol: 47.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 0.02M zinc sulphate, 25% PEG 550MME, 50mM Yb-DTPA-BMA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.28136 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2014 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28136 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→45.74 Å / Num. obs: 13205 / % possible obs: 99.8 % / Redundancy: 14 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.79→2.94 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 7.1 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.79→45.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 29.621 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.155 Å2
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Refinement step | Cycle: 1 / Resolution: 2.79→45.74 Å
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Refine LS restraints |
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