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- PDB-8hx0: Cryo-EM structure of MsDps2 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 8hx0
TitleCryo-EM structure of MsDps2 from Mycobacterium smegmatis
ComponentsPutative starvation-induced DNA protecting protein/Ferritin and Dps
KeywordsDNA BINDING PROTEIN / MsDps2 / cryo-EM
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGarg, P. / Dutta, S.
Funding support India, 2items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative starvation-induced DNA protecting protein/Ferritin and Dps
B: Putative starvation-induced DNA protecting protein/Ferritin and Dps
C: Putative starvation-induced DNA protecting protein/Ferritin and Dps
D: Putative starvation-induced DNA protecting protein/Ferritin and Dps
E: Putative starvation-induced DNA protecting protein/Ferritin and Dps
G: Putative starvation-induced DNA protecting protein/Ferritin and Dps
I: Putative starvation-induced DNA protecting protein/Ferritin and Dps
K: Putative starvation-induced DNA protecting protein/Ferritin and Dps
F: Putative starvation-induced DNA protecting protein/Ferritin and Dps
H: Putative starvation-induced DNA protecting protein/Ferritin and Dps
J: Putative starvation-induced DNA protecting protein/Ferritin and Dps
L: Putative starvation-induced DNA protecting protein/Ferritin and Dps


Theoretical massNumber of molelcules
Total (without water)214,25812
Polymers214,25812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Putative starvation-induced DNA protecting protein/Ferritin and Dps / MsDps2 / Starvation-inducible DNA-binding protein or fine tangled pili major subunit


Mass: 17854.863 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_3242, MSMEI_3159 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QXB7

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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: Cryo-EM structure of MsDps2 from Mycobacterium Smegmatis
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (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
VitrificationCryogen 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2250 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98467 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315147
ELECTRON MICROSCOPYf_angle_d0.520592
ELECTRON MICROSCOPYf_dihedral_angle_d4.3182082
ELECTRON MICROSCOPYf_chiral_restr0.0362415
ELECTRON MICROSCOPYf_plane_restr0.0042754

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