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- PDB-6f8l: Thermus thermophilus PilF ATPase (AMPPNP-bound form) -

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Basic information

Entry
Database: PDB / ID: 6f8l
TitleThermus thermophilus PilF ATPase (AMPPNP-bound form)
ComponentsType IV pilus assembly protein PilF
KeywordsMOTOR PROTEIN / type IV pilus / type II secretion / macromolecular machine
Function / homologyType II/IV secretion system protein / General secretory system II, protein E, N-terminal / P-loop containing nucleoside triphosphate hydrolase / General secretory system II, protein E, N-terminal superfamily / Type II/IV secretion system protein / Type II secretion system (T2SS), protein E, N-terminal domain / Bacterial type II secretion system protein E signature. / ATP binding / metal ion binding / Type IV pilus assembly protein PilF
Function and homology information
Specimen sourceThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8 Å resolution
AuthorsDerrick, J.P. / Collins, R.F.
CitationJournal: To Be Published
Title: To be published
Authors: Derrick, J.P. / Collins, R.F.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 13, 2017 / Release: Aug 1, 2018

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Structure visualization

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Assembly

Deposited unit
G: Type IV pilus assembly protein PilF
J: Type IV pilus assembly protein PilF
K: Type IV pilus assembly protein PilF
L: Type IV pilus assembly protein PilF
H: Type IV pilus assembly protein PilF
I: Type IV pilus assembly protein PilF
M: Type IV pilus assembly protein PilF
N: Type IV pilus assembly protein PilF
O: Type IV pilus assembly protein PilF
P: Type IV pilus assembly protein PilF
Q: Type IV pilus assembly protein PilF
R: Type IV pilus assembly protein PilF
A: Type IV pilus assembly protein PilF
B: Type IV pilus assembly protein PilF
C: Type IV pilus assembly protein PilF
D: Type IV pilus assembly protein PilF
E: Type IV pilus assembly protein PilF
F: Type IV pilus assembly protein PilF


Theoretical massNumber of molelcules
Total (without water)1,818,38318
Polyers1,818,38318
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)26240
ΔGint (kcal/M)-14
Surface area (Å2)166100
MethodPISA

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Components

#1: Protein/peptide
Type IV pilus assembly protein PilF


Mass: 101021.289 Da / Num. of mol.: 18
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLC9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Thermus thermophilus PilF ATPase (AMPPNP-bound form) / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionDetails: 25 mM HEPES pH 7.5, 150 mM NaCl, 5 mM MgCl2 and 5 % glycerol (v/v)
pH: 7.5
SpecimenConc.: 0.2 mg/ml / Details: Monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 4500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)
EM imaging opticsEnergyfilter name: k2 / Energyfilter upper: 20 eV / Energyfilter lower: 20 eV

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4EMANCTF correction
10EMANinitial Euler assignment
14RELION3D reconstruction
15RELIONCTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 450000 / Symmetry type: POINT

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