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Yorodumi- PDB-6m48: Crystal structure of pilus adhesin, SpaC from Lactobacillus rhamn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m48 | ||||||
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Title | Crystal structure of pilus adhesin, SpaC from Lactobacillus rhamnosus GG - P21212 form | ||||||
Components | SpaC | ||||||
Keywords | CELL ADHESION / Pilus adhesin / Tip pilin / vWFA domain / SpaCBA pilus / sortase / Lactobacillus rhamnosus GG / pili / fimbria / Probiotics / SpaC / lectin / surface protein / MIDAS | ||||||
Function / homology | Prealbumin-like fold domain / Prealbumin-like fold domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold / Pilus assembly protein Function and homology information | ||||||
Biological species | Lactobacillus rhamnosus GG (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kant, A. / Palva, A. / Von Ossowaski, I. / Krishnan, V. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Crystal structure of lactobacillar SpaC reveals an atypical five-domain pilus tip adhesin: Exposing its substrate-binding and assembly in SpaCBA pili. Authors: Kant, A. / Palva, A. / von Ossowski, I. / Krishnan, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m48.cif.gz | 624 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m48.ent.gz | 509.4 KB | Display | PDB format |
PDBx/mmJSON format | 6m48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m48_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6m48_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6m48_validation.xml.gz | 56.3 KB | Display | |
Data in CIF | 6m48_validation.cif.gz | 79.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/6m48 ftp://data.pdbj.org/pub/pdb/validation_reports/m4/6m48 | HTTPS FTP |
-Related structure data
Related structure data | 6m3ySC 6m7cC 7bvxC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 38 - 852 / Label seq-ID: 10 - 824
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-Components
#1: Protein | Mass: 90936.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / Gene: LGG_00444 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A1Y0DVK9 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6.5 Details: 0.25M Sodium sulphate, 0.1M BIS-Tris propane pH 6.5, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N |
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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: Apr 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→46.69 Å / Num. obs: 70856 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.057 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4503 / CC1/2: 0.718 / Rpim(I) all: 0.631 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6M3Y Resolution: 2.5→44.26 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 19.094 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.259 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.798 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→44.26 Å
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Refine LS restraints |
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