Electrostatic potential calculations with UHBD

1FTS.pdb

• description

• SRP receptor from E. coli

• expressed N and GTPase domain residues 197-497, residues 201-495 included in the structure

• solved by x-ray crystallography to 2.2 resolution

• apo, no SO₄

• Ref: Montoya, G., Svensson, C., Luirink, J., Sinning, I. Expression, crystallization and preliminary X-ray diffraction study of FtsY, the docking protein of the signal recognition particle of E. coli. (1997) Proteins 28: 285-288; Montoya, G., Svensson, C., Luirink, J., Sinning, I. Crystal structure of the NG domain from the signal-recognition particle receptor FtsY. (1997) Nature 385:365-368.

files data

• 1ftshyd.pdb (edited .pdb for UBHD: labelled OXT CTRM, labelled N terminal hydrogens NTRM, deleted last columns with atom names, used rnhyd to properly label the hydrogens for UHBD equivalence)

• ftshyd110.in (dimension of grid: 110³, spacing: 1.0 )

• ftshyd110.ou (output for above input file, charge on atom list: 0.000, Electrostatic energy when protein dielectric set to 2.0 in water of 78.0= 22757.9 kcal/mol, Electrostatic energy when protein dielectric set to 78.0 in water of 78.0= 667.161 kcal/mol

• ftshyd110.grd (ftshyd110.ins) (range: -3.93118 to +3.66443)

• ftshyd110u.grd (ftshyd110u.ins) (range: -2.75472 to +1.74055)

1FFH.pdb

• description

• SRP from Thermus aquaticus

• N and GTPase domains expressed in E. coli, residues 2-295 included in the structure

• solved by x-ray crystallography to 2.05 resolution

• 1 hydrated Mg, 124 crystallographic water molecules

• Ref: Freymann, D. M., Keenan, R. J., Stroud, R. M., Walter, P. Structure of the conserved GTPase domain of the signal recognition particle. (1997) Nature 385:361-364.

files data

• 1ffh2hyd.pdb (edited .pdb for UBHD: deleted hydrated Mg and all crystallographic water molecules, labelled OXT CTRM, added hydrogen atoms in InsightII for pH 7.0 in Charmm19 force field, deleted last columns with atom names, used rnhyd to properly label the hydrogens for UHBD equivalence)

• 1ffh2hyd110.in (dimension of grid: 110³, spacing: 1.0 )

• 1ffh2hyd110.ou (output for above input file, charge on atom list: 0.390, Electrostatic energy when protein dielectric set to 2.0 in water of 78.0= 1833.48 kcal/mol, Electrostatic energy when protein dielectric set to 78.0 in water of 78.0= 95.34 kcal/mol

• 1ffh2hyd110.grd (1ffh2hyd110.ins) (range: -1.7103 to +4.3787)

• 1ffh2hyd110u.grd (1ffh2hyd110u.ins) (range: -1.1061 to +1.4160)