|Entry||Database: PDB / ID: 5wln|
|Title||Cryo-EM structure of the T2SS secretin XcpQ from Pseudomonas aeruginosa|
|Descriptor||Type II secretion system protein D|
|Keywords||MEMBRANE PROTEIN / T2SS / Secretin / Type 2 secretion system / Pentadecamer / GspD / XcpQ|
|Specimen source||Pseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) / bacteria|
|Method||Electron microscopy (3.57 Å resolution / Particle / Single particle)|
|Authors||Hay, I.D. / Belousoff, M.J. / Lithgow, T.J.|
|Citation||MBio, 2017, 8|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 27, 2017 / Release: Oct 25, 2017|
Downloads & links
G: Type II secretion system protein D
O: Type II secretion system protein D
A: Type II secretion system protein D
B: Type II secretion system protein D
C: Type II secretion system protein D
D: Type II secretion system protein D
E: Type II secretion system protein D
F: Type II secretion system protein D
H: Type II secretion system protein D
I: Type II secretion system protein D
J: Type II secretion system protein D
K: Type II secretion system protein D
L: Type II secretion system protein D
M: Type II secretion system protein D
N: Type II secretion system protein D
Mass: 66485.656 Da / Num. of mol.: 15 / Fragment: UNP residues 35-658
Source: (gene. exp.) Pseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) / bacteria
References: UniProt: P35818
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Type 2 secretion system outer membrane secretin XcpQ / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Value: 1 deg. / Units: MEGADALTONS|
|Source (natural)||Organism: Pseudomonas aeruginosa PAO1|
|Source (recombinant)||Organism: Escherichia coli / Plasmid: pET20b / Strain: C43|
|Buffer solution||pH: 8|
|Specimen||Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil 1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Calibrated magnification: 130000 / Calibrated defocus min: 600 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|EM imaging optics||Energyfilter name: Gatan|
|Software||Name: PHENIX / Version: 1.12_2829: / Classification: refinement|
|Image processing||Details: MotionCorr 2.1|
|CTF correction||Details: CTFFIND4 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 18005|
|Symmetry||Point symmetry: C15|
|3D reconstruction||Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18005 / Number of class averages: 1 / Symmetry type: POINT|
|Atomic model building||Ref protocol: FLEXIBLE FIT|
|Refine LS restraints|
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