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- PDB-5wln: Cryo-EM structure of the T2SS secretin XcpQ from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 5wln
TitleCryo-EM structure of the T2SS secretin XcpQ from Pseudomonas aeruginosa
DescriptorType II secretion system protein D
KeywordsMEMBRANE PROTEIN / T2SS / Secretin / Type 2 secretion system / Pentadecamer / GspD / XcpQ
Specimen sourcePseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) / bacteria
MethodElectron microscopy (3.57 Å resolution / Particle / Single particle)
AuthorsHay, I.D. / Belousoff, M.J. / Lithgow, T.J.
CitationMBio, 2017, 8

MBio, 2017, 8 Yorodumi Papers
Structural Basis of Type 2 Secretion System Engagement between the Inner and Outer Bacterial Membranes.
Iain D Hay / Matthew J Belousoff / Trevor Lithgow

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 27, 2017 / Release: Oct 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2017Structure modelrepositoryInitial release
1.1Nov 1, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)997,28515
Polyers997,28515
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)
Type II secretion system protein D / T2SS protein D / General secretion pathway 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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Type 2 secretion system outer membrane secretin XcpQ / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 1 deg. / Units: MEGADALTONS
Source (natural)Organism: Pseudomonas aeruginosa PAO1
Source (recombinant)Organism: Escherichia coli / Plasmid: pET20b / Strain: C43
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMHEPES1
2300mMNaCl1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil 1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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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 / Calibrated magnification: 130000 / Calibrated defocus min: 600 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: Gatan

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDFitting ID
4CTFFIND4CTF CORRECTION1
7NAMD2.12MODEL FITTING1
9PHENIX1.12MODEL REFINEMENT1
10cryoSPARC0.4.1INITIAL EULER ASSIGNMENT1
11cryoSPARC0.4.1FINAL EULER ASSIGNMENT1
12cryoSPARC0.4.1CLASSIFICATION1
13cryoSPARC0.4.1RECONSTRUCTION1
Image processingDetails: MotionCorr 2.1
CTF correctionDetails: CTFFIND4 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 18005
SymmetryPoint symmetry: C15
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18005 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01252665
ELECTRON MICROSCOPYf_angle_d1.30071475
ELECTRON MICROSCOPYf_dihedral_angle_d7.05932685
ELECTRON MICROSCOPYf_chiral_restr0.0728835
ELECTRON MICROSCOPYf_plane_restr0.0099345

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