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- EMDB-35070: Cryo-EM structure of MsDps2 from Mycobacterium smegmatis -

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Basic information

Entry
Database: EMDB / ID: EMD-35070
TitleCryo-EM structure of MsDps2 from Mycobacterium smegmatis
Map data
Sample
  • Complex: Cryo-EM structure of MsDps2 from Mycobacterium Smegmatis
    • Protein or peptide: Putative starvation-induced DNA protecting protein/Ferritin and Dps
KeywordsMsDps2 / cryo-EM / DNA BINDING PROTEIN
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding
Similarity search - Function
Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Starvation-inducible DNA-binding protein or fine tangled pili major subunit
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGarg P / Dutta S
Funding support India, 2 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Department of Science & Technology (DST, India) India
CitationJournal: To Be Published
Title: Cryo-EM structure of MsDps2 from Mycobacterium smegmatis
Authors: Garg P / Dutta S
History
DepositionJan 3, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_35070.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.74 Å
Density
Contour LevelBy AUTHOR: 0.614
Minimum - Maximum-2.5640628 - 3.3071215
Average (Standard dev.)-0.0007972413 (±0.12457459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 242.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of MsDps2 from Mycobacterium Smegmatis

EntireName: Cryo-EM structure of MsDps2 from Mycobacterium Smegmatis
Components
  • Complex: Cryo-EM structure of MsDps2 from Mycobacterium Smegmatis
    • Protein or peptide: Putative starvation-induced DNA protecting protein/Ferritin and Dps

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Supramolecule #1: Cryo-EM structure of MsDps2 from Mycobacterium Smegmatis

SupramoleculeName: Cryo-EM structure of MsDps2 from Mycobacterium Smegmatis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: Putative starvation-induced DNA protecting protein/Ferritin and Dps

MacromoleculeName: Putative starvation-induced DNA protecting protein/Ferritin and Dps
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 17.854863 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSARRTESDI QGFHATPEFG GNLQKVLVDL IELSLQGKQA HWNVVGSNFR DLHLQLDELV DFAREGSDTI AERMRALDAV PDGRSDTVA ATTTLPEFPA FERSTADVVD LITTRINATV DTIRRVHDAV DAEDPSTADL LHGLIDGLEK QAWLIRSENR K V

UniProtKB: Starvation-inducible DNA-binding protein or fine tangled pili major subunit

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2z90

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98467
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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