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Yorodumi- PDB-6t8s: Structure of the major Type IV pilin PilA1 from Clostridium difficile -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t8s | ||||||
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Title | Structure of the major Type IV pilin PilA1 from Clostridium difficile | ||||||
Components | Pilin | ||||||
Keywords | PROTEIN FIBRIL / Pillin / Type IV Pillin | ||||||
Function / homology | Bacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / protein secretion by the type II secretion system / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / type II protein secretion system complex / membrane => GO:0016020 / Pilin Function and homology information | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.65 Å | ||||||
Authors | Crawshaw, A.D. / Basle, A. / Salgado, P.S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study. Authors: Crawshaw, A.D. / Basle, A. / Salgado, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t8s.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t8s.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6t8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/6t8s ftp://data.pdbj.org/pub/pdb/validation_reports/t8/6t8s | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 15910.838 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) Gene: pilE1, SAMEA840506_01547, SAMEA897066_02999, SAMEA897109_03172, SAMEA897162_02309 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A449M2W4 #2: Water | ChemComp-HOH / | |
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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: 2.87 Å3/Da / Density % sol: 57.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 26, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→73.25 Å / Num. obs: 67404 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.037 / Rrim(I) all: 0.14 / Net I/σ(I): 12 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.65→73.25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.204 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.082 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 116.35 Å2 / Biso mean: 26.4 Å2 / Biso min: 15.74 Å2
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Refinement step | Cycle: final / Resolution: 1.65→73.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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