[English] 日本語
Yorodumi- PDB-6to1: Crystal structure of three N-terminal domains of the type V pili ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6to1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of three N-terminal domains of the type V pili tip protein Mfa5 from Porphyromonas gingivalis | |||||||||
Components | Minor fimbrium subunit Mfa5 | |||||||||
Keywords | CELL ADHESION / Intramolekular Isopeptide / von Willebrand factor / Bacterial adhesion / P. gingivalis / Mfa1 fimbriae / Type V pili | |||||||||
Function / homology | von Willebrand factor type A domain / pilus / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / PHOSPHATE ION / Minor fimbrium subunit Mfa5 Function and homology information | |||||||||
Biological species | Porphyromonas gingivalis ATCC 33277 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Persson, K. / Heidler, T.V. | |||||||||
Funding support | Sweden, 2items
| |||||||||
Citation | Journal: Commun Biol / Year: 2021 Title: Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide. Authors: Heidler, T.V. / Ernits, K. / Ziolkowska, A. / Claesson, R. / Persson, K. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6to1.cif.gz | 300 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6to1.ent.gz | 191.9 KB | Display | PDB format |
PDBx/mmJSON format | 6to1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6to1_validation.pdf.gz | 440.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6to1_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 6to1_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 6to1_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/6to1 ftp://data.pdbj.org/pub/pdb/validation_reports/to/6to1 | HTTPS FTP |
-Related structure data
Related structure data | 6tnjSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 112438.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GAM = expression Tag Remaining amino acids are 21-1044 of Mfa5 Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria) Gene: PGN_0291 / Plasmid: pET / Details (production host): Hisx6_ZZ_GS_Tev / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: B2RHG5 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-MG / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.39 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 17% PEG3350, 80mM NaPO4 pH6, 3mM CaCL and 3mM MgCL |
-Data collection
Diffraction | Mean temperature: 290 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9756 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016 / Details: Sagitally bended Si111 crystal |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→46.98 Å / Num. obs: 64113 / % possible obs: 99.45 % / Redundancy: 13.1 % / Biso Wilson estimate: 23.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09715 / Rpim(I) all: 0.02756 / Rrim(I) all: 0.1011 / Net I/σ(I): 19.66 |
Reflection shell | Resolution: 1.799→1.863 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.126 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 6117 / CC1/2: 0.646 / Rpim(I) all: 0.3445 / Rrim(I) all: 1.18 / % possible all: 95.94 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TNJ Resolution: 1.8→46.98 Å / SU ML: 0.1642 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1022
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|