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- PDB-5n8n: Contracted sheath of a Pseudomonas aeruginosa type six secretion ... -

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Basic information

Entry
Database: PDB / ID: 5n8n
TitleContracted sheath of a Pseudomonas aeruginosa type six secretion system consisting of TssB1 and TssC1
DescriptorType VI secretion protein
family
EvpB family type VI secretion protein
KeywordsSTRUCTURAL PROTEIN / type six secretion system / structural protein
Specimen sourcePseudomonas aeruginosa / bacteria / シュードモナス・エルジノーサ, 緑膿菌
MethodElectron microscopy (3.28 Å resolution / Helical array / Helical)
AuthorsSalih, O. / He, S. / Stach, L. / Macdonald, J.T. / Planamente, S. / Manoli, E. / Scheres, S. / Filloux, A. / Freemont, P.S.
CitationStructure, 2017

Structure, 2017 Yorodumi Papers
Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa.
Osman Salih / Shaoda He / Sara Planamente / Lasse Stach / James T MacDonald / Eleni Manoli / Sjors H W Scheres / Alain Filloux / Paul S Freemont

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 23, 2017 / Release: Jan 10, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 10, 2018Structure modelrepositoryInitial release
1.1Jan 17, 2018Structure modelDatabase referencescitation / citation_author_citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Assembly

Deposited unit
A: Type VI secretion protein, family
B: EvpB family type VI secretion protein
C: Type VI secretion protein, family
D: EvpB family type VI secretion protein
E: Type VI secretion protein, family
F: EvpB family type VI secretion protein
G: Type VI secretion protein, family
H: EvpB family type VI secretion protein
I: Type VI secretion protein, family
J: EvpB family type VI secretion protein
K: Type VI secretion protein, family
L: EvpB family type VI secretion protein
M: Type VI secretion protein, family
N: EvpB family type VI secretion protein
O: Type VI secretion protein, family
P: EvpB family type VI secretion protein
Q: Type VI secretion protein, family
R: EvpB family type VI secretion protein
S: Type VI secretion protein, family
T: EvpB family type VI secretion protein
U: Type VI secretion protein, family
V: EvpB family type VI secretion protein
W: Type VI secretion protein, family
X: EvpB family type VI secretion protein
Y: Type VI secretion protein, family
Z: EvpB family type VI secretion protein
a: Type VI secretion protein, family
b: EvpB family type VI secretion protein
c: Type VI secretion protein, family
d: EvpB family type VI secretion protein


Theoretical massNumber of molelcules
Total (without water)995,33830
Polyers995,33830
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)201830
ΔGint (kcal/M)-1170
Surface area (Å2)378640
MethodPISA

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Components

#1: Polypeptide(L)
Type VI secretion protein, family


Mass: 14634.741 Da / Num. of mol.: 15
Source: (gene. exp.) Pseudomonas aeruginosa / bacteria / シュードモナス・エルジノーサ, 緑膿菌
References: UniProt: A0A072ZG09
#2: Polypeptide(L)
EvpB family type VI secretion protein


Mass: 51721.125 Da / Num. of mol.: 15
Source: (gene. exp.) Pseudomonas aeruginosa / bacteria / シュードモナス・エルジノーサ, 緑膿菌
References: UniProt: A0A0E1AL03

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1contracted sheath of a Pseudomonas aeruginosa T6SS consisting of TssB1 and TssC1COMPLEX1, 20RECOMBINANT
2AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_17_VIM_2_10_11_02574, PAMH19_0082COMPLEX11RECOMBINANT
3U769_00445COMPLEX21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12287Pseudomonas aeruginosa
23287Pseudomonas aeruginosa
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli
23562Escherichia coli
Buffer solutionpH: 9
SpecimenConc.: 1 mg/ml / 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 27.7 deg. / Axial rise/subunit: 20.2 Å / Axial symmetry: C1
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 71264 / Symmetry type: HELICAL

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