› 5o58

X-ray diffraction
1.55Å resolution

Structure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApG

Released:
DOI: 10.2210/pdb5o58/pdb
PDB entry 5o58 coloured by chain, front view.
PDB entry 5o58 coloured by chain, side view.
PDB entry 5o58 coloured by chain, top view.
Source organisms:
Primary publication:
Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.
Drexler DJ, Müller M, Rojas-Cordova CA, Bandera AM, Witte G
Structure 25 1887-1897.e4 (2017)
PMID: 29107484

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194832 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
phosphodiesterase TM1595 Chain: A
Molecule details ›
Chain: A
Length: 338 amino acids
Theoretical weight: 37.87 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X1T1 (Residues: 1-333; Coverage: 100%)
Gene name: TM_1595
Sequence domains:
RNA (5'-R(P*AP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 2 nucleotides
Theoretical weight: 629 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand EDO 18 x EDO
Ligand IPA 5 x IPA
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: C2221
Unit cell:
a: 70.37Å b: 88.34Å c: 124.27Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.159 0.158 0.184
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms.
He et al. (2020)
1 more

1 mention without citation

Making and Breaking of an Essential Poison: the Cyclases and Phosphodiesterases That Produce and Degrade the Essential Second Messenger Cyclic di-AMP in Bacteria.
Commichau et al. (2019)