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- PDB-5wda: Structure of the PulG pseudopilus -

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Basic information

Entry
Database: PDB / ID: 5wda
TitleStructure of the PulG pseudopilus
DescriptorGeneral secretion pathway protein G
KeywordsPROTEIN TRANSPORT / helical polymer / bacterial secretion / cryo-EM
Specimen sourceKlebsiella oxytoca / bacteria / クレブシエラ・オキシトカ
MethodElectron microscopy (5 Å resolution / Filament / Helical)
AuthorsLopez-Castilla, A. / Thomassin, J.L. / Bardiaux, B. / Zheng, W. / Nivaskumar, M. / Yu, X. / Nilges, M. / Egelman, E.H. / Izadi-Pruneyre, N. / Francetic, O.
CitationNat Microbiol, 2017

Nat Microbiol, 2017 Yorodumi Papers
Structure of the calcium-dependent type 2 secretion pseudopilus.
Aracelys López-Castilla / Jenny-Lee Thomassin / Benjamin Bardiaux / Weili Zheng / Mangayarkarasi Nivaskumar / Xiong Yu / Michael Nilges / Edward H Egelman / Nadia Izadi-Pruneyre / Olivera Francetic

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 4, 2017 / Release: Oct 25, 2017

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Assembly

Deposited unit
A: General secretion pathway protein G
B: General secretion pathway protein G
C: General secretion pathway protein G
D: General secretion pathway protein G
E: General secretion pathway protein G
F: General secretion pathway protein G
G: General secretion pathway protein G
H: General secretion pathway protein G
I: General secretion pathway protein G
J: General secretion pathway protein G
K: General secretion pathway protein G
L: General secretion pathway protein G
M: General secretion pathway protein G
N: General secretion pathway protein G
O: General secretion pathway protein G
P: General secretion pathway protein G
Q: General secretion pathway protein G
R: General secretion pathway protein G
S: General secretion pathway protein G
T: General secretion pathway protein G
U: General secretion pathway protein G
V: General secretion pathway protein G
W: General secretion pathway protein G
X: General secretion pathway protein G
Y: General secretion pathway protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,13950
Polyers363,13725
Non-polymers1,00225
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)89630
ΔGint (kcal/M)-692
Surface area (Å2)128840

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Components

#1: Polypeptide(L) ...
General secretion pathway protein G / General secretion pathway protein GspG


Mass: 14525.482 Da / Num. of mol.: 25 / Fragment: UNP residues 7-140
Source: (gene. exp.) Klebsiella oxytoca / bacteria / クレブシエラ・オキシトカ
References: UniProt: A0A0G3SCW3
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 25 / Formula: Ca

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: PulG pseudopilus / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella oxytoca
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1819

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameCategoryImage processing ID
4CTFFIND3CTF CORRECTION1
13IHRSRRECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 83.2 deg. / Axial rise/subunit: 10.2 Å / Axial symmetry: C1
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 85619 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01249625
ELECTRON MICROSCOPYf_angle_d1.43190250
ELECTRON MICROSCOPYf_dihedral_angle_d3.06419400
ELECTRON MICROSCOPYf_chiral_restr0.0683900
ELECTRON MICROSCOPYf_plane_restr0.00811075

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