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- PDB-8x1i: ParM present of genome of Desufitobacterium hafniense - Dh-cParM1 -

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Basic information

Entry
Database: PDB / ID: 8x1i
TitleParM present of genome of Desufitobacterium hafniense - Dh-cParM1
ComponentsParM present of genome of Desufitobacterium hafniense - Dh-cParM1
KeywordsSTRUCTURAL PROTEIN / ParM / genome / segregation / plasmid
Function / homology: / Archaeal actin homologue MreB-like, C-terminal / ParM-like / Actin-like protein, N-terminal / Actin like proteins N terminal domain / ATPase, nucleotide binding domain / ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein
Function and homology information
Biological speciesDesulfitobacterium hafniense Y51 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å
AuthorsAli, S. / Robinson, R.C. / Narita, A.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Society for the Promotion of Science (JSPS)18H02410 Japan
Japan Society for the Promotion of Science (JSPS)21H02440 Japan
CitationJournal: To Be Published
Title: Bacterial genome encoded ParMs
Authors: Ali, S. / Robinson, R.C. / Narita, A.
History
DepositionNov 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ParM present of genome of Desufitobacterium hafniense - Dh-cParM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0443
Polymers40,5921
Non-polymers4522
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ParM present of genome of Desufitobacterium hafniense - Dh-cParM1


Mass: 40592.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: genome encode ParM1 from Desulfitobacterium species
Source: (gene. exp.) Desulfitobacterium hafniense Y51 (bacteria)
Gene: DSY2109 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q24VP4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Dh-cParM1 / Type: ORGANELLE OR CELLULAR COMPONENT
Details: ParM present of genome of Desufitobacterium hafniense - Dh-cParM1
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.405 kDa/nm / Experimental value: YES
Source (natural)Organism: Desulfitobacterium hafniense Y51 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: PSY5
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: ParM present of genome of Desufitobacterium hafniense - Dc-cParM1
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4RELION3.1/4.0CTF correctionGctf incorporated RELION was used for CFT determination and correction
7UCSF Chimeramodel fitting
9ISOLDEmodel refinement
12RELION3.1/4.0classification
13RELION3.1/4.03D reconstruction3D structure was reconstructed using RELION software
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 156.03 ° / Axial rise/subunit: 24.5 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 2500
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2100 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial fitting was performed using chimera and MDFF performed by ISOLDE and final real space refine by Phenix real space refinement.
Atomic model buildingSource name: AlphaFold / Type: in silico model

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