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- PDB-6wkv: Cryo-EM structure of engineered variant of the Encapsulin from Th... -

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Basic information

Entry
Database: PDB / ID: 6wkv
TitleCryo-EM structure of engineered variant of the Encapsulin from Thermotoga maritima (TmE)
ComponentsEncapsulin
KeywordsHYDROLASE / Proteolysis / Cytolysis / Defense Response to Bacterium / Extracellular Region
Function / homology
Function and homology information


encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / iron ion transport / intracellular iron ion homeostasis / proteolysis
Similarity search - Function
Type 1 encapsulin shell protein / Encapsulating protein for peroxidase
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Type 1 encapsulin shell protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsWilliams, E. / Jenkins, M. / Zhao, H. / Juneja, P. / Lutz, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)US-NSF (CBET 1706891) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of engineered variant of the Encapsulin from Thermotoga maritima (TmE)
Authors: Williams, E. / Zhao, H. / Jenkins, M. / Juneja, P. / Lutz, S.
History
DepositionApr 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Encapsulin
B: Encapsulin
C: Encapsulin
D: Encapsulin
E: Encapsulin
F: Encapsulin
G: Encapsulin
H: Encapsulin
I: Encapsulin
J: Encapsulin
K: Encapsulin
L: Encapsulin
M: Encapsulin
N: Encapsulin
O: Encapsulin
P: Encapsulin
Q: Encapsulin
R: Encapsulin
S: Encapsulin
T: Encapsulin
U: Encapsulin
V: Encapsulin
W: Encapsulin
X: Encapsulin
Y: Encapsulin
Z: Encapsulin
0: Encapsulin
1: Encapsulin
2: Encapsulin
3: Encapsulin
4: Encapsulin
5: Encapsulin
6: Encapsulin
7: Encapsulin
8: Encapsulin
9: Encapsulin
a: Encapsulin
b: Encapsulin
c: Encapsulin
d: Encapsulin
e: Encapsulin
f: Encapsulin
g: Encapsulin
h: Encapsulin
i: Encapsulin
j: Encapsulin
k: Encapsulin
l: Encapsulin
m: Encapsulin
n: Encapsulin
o: Encapsulin
p: Encapsulin
q: Encapsulin
r: Encapsulin
s: Encapsulin
t: Encapsulin
u: Encapsulin
v: Encapsulin
w: Encapsulin
x: Encapsulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,803,607120
Polymers1,776,22660
Non-polymers27,38160
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area288270 Å2
ΔGint-584 kcal/mol
Surface area584300 Å2

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Components

#1: Protein ...
Encapsulin / Thermotoga bacteriocin / Maritimacin


Mass: 29603.766 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0785 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9WZP2, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical...
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C17H21N4O9P
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mutant Enapsulin protein / Type: COMPLEX / Details: FMN bound to Encapsulin / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Thermotoga maritima (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Image recordingElectron dose: 54 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.16_3549refinement
PHENIX1.16_3549refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPU1.1image acquisition
10RELION3.1initial Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 69476
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24401 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32.05 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0077130200
ELECTRON MICROSCOPYf_angle_d0.6178176880
ELECTRON MICROSCOPYf_chiral_restr0.048219200
ELECTRON MICROSCOPYf_plane_restr0.003522200
ELECTRON MICROSCOPYf_dihedral_angle_d16.977476920

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