ISDA

Deposition Date 2024-07-26

Release Date 2025-01-01

Last Version Date 2025-01-01

Entry Detail

PDB ID:

9IX4

Keywords:

DNA BINDING PROTEIN/DNA

Title:

Cryo-EM structure of Lactobacillus casei DdmD dimer bound with DNA

Biological Source:

Source Organism:

Lacticaseibacillus (Taxon ID: 2759736)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.96 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DdmD
Gene (Uniprot):FEI15_05225
Chain IDs:A, C (auth: B)
Chain Length:1192
Number of Molecules:2
Biological Source:Lacticaseibacillus

UniProt ID:A0A5R8LS59

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:Lacticaseibacillus

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
Chain IDs:D
Chain Length:12
Number of Molecules:1
Biological Source:Lacticaseibacillus

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Chain IDs:E, F
Chain Length:10
Number of Molecules:2
Biological Source:Lacticaseibacillus

Ligand Molecules

ADP

Primary Citation

The mechanism of bacterial defense system DdmDE from Lactobacillus casei.

Huang, P, Yan, P, Guo, L, Fei, W, Li, Z, Liu, J, Kong, J, Yao, Y, Lu, M, Xiao, Y, Chen, M.Show

Cell Res. 34 873 876 (2024)

PMID: 39448873 DOI: 10.1038/s41422-024-01042-y

Primary Citation of related structures