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Yorodumi- PDB-6bbk: N-terminally truncated group I PilA from Pseudomonas aeruginosa s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bbk | ||||||
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Title | N-terminally truncated group I PilA from Pseudomonas aeruginosa strain 1244 | ||||||
Components | Fimbrial protein | ||||||
Keywords | MEMBRANE PROTEIN / Pseudomonas aeruginosa / type IV pili / major pilin / pilin / pilus / twitching motility / adhesion / biofilm / virulence / filament / subunit | ||||||
Function / homology | Function and homology information protein secretion by the type II secretion system / type II protein secretion system complex / pilus / membrane => GO:0016020 / cell adhesion Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.73 Å | ||||||
Authors | Shen, Y. / Guarne, A. / Nguyen, Y. / Burrows, L.L. | ||||||
Citation | Journal: To Be Published Title: N-terminally truncated group I PilA from Pseudomonas aeruginosa strain 1244 Authors: Shen, Y. / Nguyen, Y. / Guarne, A. / Burrows, L.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bbk.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bbk.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 6bbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bbk_validation.pdf.gz | 413.9 KB | Display | wwPDB validaton report |
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Full document | 6bbk_full_validation.pdf.gz | 413.9 KB | Display | |
Data in XML | 6bbk_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 6bbk_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/6bbk ftp://data.pdbj.org/pub/pdb/validation_reports/bb/6bbk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13202.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pilA, fimA / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 / Variant (production host): non-reducing cytoplasm / References: UniProt: P18774 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES:NaOH, 20% (w/v) PEG 4000, 10% (v/v) 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→35 Å / Num. obs: 12215 / % possible obs: 98.8 % / Redundancy: 35.6 % / Biso Wilson estimate: 21.21 Å2 / Rmerge(I) obs: 0.051 / Χ2: 0.982 / Net I/σ(I): 19 / Num. measured all: 434970 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.73→29.554 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.73 Å2 / Biso mean: 22.5606 Å2 / Biso min: 11.54 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.73→29.554 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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