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- PDB-9rkt: Agrobacterium phage 7-7-1 collar -

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Basic information

Entry
Database: PDB / ID: 9rkt
TitleAgrobacterium phage 7-7-1 collar
ComponentsStructural protein
KeywordsVIRUS / Flagella phage / Agrobacterium sp. H13-3 / Collar
Function / homologyStructural protein
Function and homology information
Biological speciesAgrobacterium phage 7-7-1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsNoteborn, W.E.M. / Hoeksma, T. / Briegel, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: To Be Published
Title: Using cryogenic electron micrography methods to gain insight into structure and initial host attachment of the fagellotrophic bacteriophage 7-7-1
Authors: Noteborn, W.E.M. / Hoeksma, T. / Briegel, A.
History
DepositionJun 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,491,23160
Polymers1,491,23160
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Structural protein


Mass: 24853.850 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7FAG1
Has protein modificationN

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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: Agrobacterium phage 7-7-1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C15 (15 fold cyclic)
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4792 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 90.56 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002497980
ELECTRON MICROSCOPYf_angle_d0.4575134040
ELECTRON MICROSCOPYf_chiral_restr0.045914760
ELECTRON MICROSCOPYf_plane_restr0.003818000
ELECTRON MICROSCOPYf_dihedral_angle_d4.25213500

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