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(12):1887-1897.e4 (2017) Europe PMC

SASDCD7 – Thermotoga maritima phosphodiesterase TM1595 (wildtype, TmPde)

Thermotoga maritima phosphodiesterase (wildtype, TmPDE, TM1595)

MW^experimental	67	kDa
MW^expected	76	kDa
V^Porod	106	nm³

log I(s) 1.97×10⁴ 1.97×10³ 1.97×10² 1.97×10¹

Thermotoga maritima phosphodiesterase (wildtype, TmPDE, TM1595) small angle scattering data

s, nm^-1

Log plot Log-Log plot

ln I(s)

Thermotoga maritima phosphodiesterase (wildtype, TmPDE, TM1595) Guinier plot

ln 1.98×10⁴ R_g: 2.7 nm 0 (2.7 nm)^-2 s²

(sR_g)²I(s)/I(0)

Thermotoga maritima phosphodiesterase (wildtype, TmPDE, TM1595) Kratky plot

1.104 0 √3 sR_g

p(r)	R_g: 2.7 nm 0 D_max: 7.8 nm

Data validation

Experimental data range

p(r) fit to data

Metric

Value

s_min D_max / π

0.2

N_Shannon

Worse

Better

Metric

Value

p_cormap

χ²

0
1.580

Worse

Better

Fits and models

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

Thermotoga maritima phosphodiesterase (wildtype, TmPDE, TM1595) PDB (PROTEIN DATA BANK) model

Synchrotron SAXS data from solutions of Thermotoga maritima phosphodiesterase TM1595 (wildtype, TmPde) in 20mM Tris, 200 mM NaCl, 5%(v/v) glycerol, pH 7.5, were collected on the EMBL-P12 beam line on the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123987 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). One solute concentration of 7.00 mg/ml was measured at 20°C. 34 successive 0.045 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration.

Storage temperature = UNKNOWN

Thermotoga maritima phosphodiesterase (wildtype, TmPDE, TM1595) (TmPde)
Mol. type		Protein
Organism		Thermotoga maritima
Olig. state		Dimer
Mon. MW		37.8 kDa

UniProt		Q9X1T1
Sequence		FASTA

PDB ID		5O25