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- PDB-5wjz: Cryo-EM structure of B. subtilis flagellar filaments E115G -

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Basic information

Entry
Database: PDB / ID: 5wjz
TitleCryo-EM structure of B. subtilis flagellar filaments E115G
DescriptorFlagellin
KeywordsPROTEIN FIBRIL / bacteria flagella / helical polymers / cryo-EM
Specimen sourceBacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /
MethodElectron microscopy (5.7 Å resolution / Filament / Helical)
AuthorsWang, F. / Burrage, A.M. / Orlova, A. / Kearns, D.B. / Egelman, E.H.
CitationNat Commun, 2017, 8, 960-960

Nat Commun, 2017, 8, 960-960 Yorodumi Papers
A structural model of flagellar filament switching across multiple bacterial species.
Fengbin Wang / Andrew M Burrage / Sandra Postel / Reece E Clark / Albina Orlova / Eric J Sundberg / Daniel B Kearns / Edward H Egelman

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 24, 2017 / Release: Oct 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2017Structure modelrepositoryInitial release
1.1Nov 1, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

Deposited unit
A: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
Q: Flagellin
R: Flagellin
S: Flagellin
T: Flagellin
U: Flagellin
V: Flagellin
W: Flagellin
X: Flagellin
Y: Flagellin
Z: Flagellin
a: Flagellin
b: Flagellin
c: Flagellin
d: Flagellin
e: Flagellin
f: Flagellin
g: Flagellin
h: Flagellin
i: Flagellin
j: Flagellin
k: Flagellin
l: Flagellin
m: Flagellin
n: Flagellin
o: Flagellin
p: Flagellin
q: Flagellin
r: Flagellin
s: Flagellin
t: Flagellin


Theoretical massNumber of molelcules
Total (without water)1,499,10446
Polyers1,499,10446
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)333270
ΔGint (kcal/M)-1183
Surface area (Å2)465050

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Components

#1: Polypeptide(L) ...
Flagellin


Mass: 32589.223 Da / Num. of mol.: 46 / Mutation: E115G,T209C
Source: (gene. exp.) Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /
References: UniProt: A0A162QQD4

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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: Bacillus subtilis flagella filament / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus subtilis
Source (recombinant)Organism: Bacillus subtilis
Buffer solutionDetails: Imidazole buffer / pH: 6.8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: negative stain
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 %

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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 recordingAverage exposure time: 2 sec. / Electron dose: 20 e/Å2
Details: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the estimation of the CTF as well as for boxing filaments. Only the first two parts were used for the reconstruction (~5 electrons per Angstrom^2).
Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

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Processing

SoftwareName: PHENIX / Version: dev_2471: / Classification: refinement
EM software
IDNameCategoryImage processing IDImaging IDFitting ID
1EMAN2PARTICLE SELECTION1
2EPUIMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
7RosettaMODEL FITTING1
9SPIDERINITIAL EULER ASSIGNMENT1
10SPIDERFINAL EULER ASSIGNMENT1
11SPIDERCLASSIFICATION1
12SPIDERRECONSTRUCTION1
13PHENIXMODEL REFINEMENT1
14CootMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.3 deg. / Axial rise/subunit: 4.72 Å / Axial symmetry: C1
3D reconstructionResolution: 5.7 Å / Resolution method: OTHER / Number of particles: 22682 / Algorithm: BACK PROJECTION / Details: model-map FSC 0.38 cut-off / Symmetry type: HELICAL
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007207828
ELECTRON MICROSCOPYf_angle_d1.157375222
ELECTRON MICROSCOPYf_dihedral_angle_d3.88382064
ELECTRON MICROSCOPYf_chiral_restr0.05116744
ELECTRON MICROSCOPYf_plane_restr0.00535236

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