› 3rmp

X-ray diffraction
2.21Å resolution

Structural basis for the recognition of attP substrates by P4-like integrases

Released:
DOI: 10.2210/pdb3rmp/pdb
PDB entry 3rmp coloured by chain, front view.
PDB entry 3rmp coloured by chain, side view.
PDB entry 3rmp coloured by chain, top view.
Source organism: Yersinia pestis
Entry authors: Szwagierczak A, Popowicz GM, Holak TA, Rakin A, Antonenka U

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116832 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
CP4-like integrase Chains: A, C
Molecule details ›
Chains: A, C
Length: 88 amino acids
Theoretical weight: 10.1 KDa
Source organism: Yersinia pestis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9Z3B4 (Residues: 1-80; Coverage: 19%)
Gene names: YPO1917, int
Sequence domains: Arm DNA-binding domain
Structure domains: Integrase, DNA-binding domain
5'-D(*TP*AP*AP*TP*GP*AP*CP*CP*AP*CP*CP*AP*AP*TP*A)-3' Chains: E, G
Molecule details ›
Chains: E, G
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
Source organism: Yersinia pestis
Expression system: Not provided
5'-D(*TP*AP*TP*TP*GP*GP*TP*GP*GP*TP*CP*AP*TP*TP*A)-3' Chains: F, H
Molecule details ›
Chains: F, H
Length: 15 nucleotides
Theoretical weight: 4.63 KDa
Source organism: Yersinia pestis
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 60.9Å b: 69.49Å c: 83.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.234 0.28
Expression systems:
  • Escherichia coli BL21
  • Not provided

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