› 5f8a

X-ray diffraction
1.76Å resolution

Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV-DNA complex inhibits cleavage.

Released:
DOI: 10.2210/pdb5f8a/pdb
PDB entry 5f8a coloured by chain, front view.
PDB entry 5f8a coloured by chain, side view.
PDB entry 5f8a coloured by chain, top view.
Source organisms:
Primary publication:
Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex.
Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson L
Biochemistry 55 6115-6132 (2016)
PMID: 27786446

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118662 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Type II restriction enzyme EcoRV Chains: A, B
Molecule details ›
Chains: A, B
Length: 244 amino acids
Theoretical weight: 28.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P04390 (Residues: 2-245; Coverage: 100%)
Gene name: ecoRVR
Sequence domains: Restriction endonuclease EcoRV
Structure domains: DNA mismatch repair MutH/Restriction endonuclease, type II
DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*T)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand LU 2 x LU
Ligand NA 2 x NA
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E DW
Spacegroup: P1
Unit cell:
a: 46.43Å b: 52.86Å c: 65.31Å
α: 70.61° β: 73.24° γ: 81.81°
R-values:
R R work R free
0.164 0.16 0.199
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

NMR-based investigations into target DNA search processes of proteins.
Iwahara et al. (2018)
1 other article

1 mention without citation

Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex.
Sinha et al. (2016)