| Gene (Deinococcus radiodurans) |
DraNramp |
Genomic DNA |
Uniprot: Q9RTP8
|
|
| Strain, strain background (Escherichia coli) |
C41(DE3) |
Lucigen |
60442–1 |
Chemically competent cells |
| Strain, strain background (Escherichia coli) |
DH5α |
Invitrogen |
18265–017 |
Chemically competent cells |
| Recombinant DNA reagent |
pET21a |
Novagen |
69740–3 |
Vector backbone for cloning DraNramp |
| Chemical compound, drug |
n-Dodecyl-β-D-Maltopyranoside |
Anatrace |
D310S |
1% for solubilizing membrane, 0.03% used in wash buffer |
| Chemical compound, drug |
n-Decyl-β-D-Maltopyranoside |
Anatrace |
D322S |
0.1% used in exchange buffer |
| Chemical compound, drug |
Lauryl maltose neopentyl glycol |
Anatrace |
NG310
|
0.01% in elution buffer, 0.003% used in SEC buffer |
| Chemical compound, drug |
Monoolein |
Anatrace |
LCP18
|
1:1.5 (protein: monoolein) for LCP crystallization |
| Chemical compound, drug |
Fura-2 Pentapotassium Salt, cell impermeant |
Life Technologies |
F-1200
|
5 mM mixed with in proteoliposome |
| Chemical compound, drug |
1-Palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) |
Avanti Polar Lipids |
850457 C |
lipid mixture (3 POPE: 1 POPG) and protein in 400:1 ratio for proteoliposome preparation |
| Chemical compound, drug |
1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) |
Avanti Polar Lipids |
840757 C |
lipid mixture (3 POPE: 1 POPG) and protein in 400:1 ratio for proteoliposome preparation |
| Chemical compound, drug |
Valinomycin |
Sigma-Aldrich |
V0627 |
Creates membrane potential by transporting K+ in proteoliposome assay |
| Commercial assay, kit |
Ni Sepharose High Performance Resin |
Cytiva |
95055–838 |
IMAC resin |
| Commercial assay, kit |
Superdex 200 10/300 GL |
Cytiva |
89497–272 |
SEC column |
| Commercial assay, kit |
PD-10 Desalting Column |
Cytiva |
95017–001 |
Buffer exchange |
| Software, algorithm |
XDS |
PMID:20124692
|
RRID:SCR_015652
|
Data Porcessing |
| Software, algorithm |
PHASER |
PMID:19461840
|
RRID:SCR_014219
|
Model Builiding |
| Software, algorithm |
PHENIX |
PMID:22505256
|
RRID:SCR_014224
|
Refinement |
| Software, algorithm |
coot |
PMID:20383002
|
RRID:SCR_014222
|
Refinement and model building |
| Software, algorithm |
PyMOL |
Schrödinger |
RRID:SCR_000305
|
Figure making |
| Software, algorithm |
HMMER |
hmmer.org |
RRID:SCR_005305
|
Collected sequences with jackhmmer and aligned with hmmalign |
| Software, algorithm |
MUSCLE |
PMID:15318951
|
RRID:SCR_011812
|
Aligning sequences |
| Software, algorithm |
RAxML-NG |
PMID:31070718
|
RRID:SCR_022066
|
Tree building |
| Software, algorithm |
PropKa |
PMID:26596171
|
|
Identifying protonation states |
| Software, algorithm |
CHARMM-GUI |
PMID:25130509
|
|
Building MD system |
| Software, algorithm |
NAMD |
PMID:20675161
|
RRID:SCR_014894
|
Running MD simulations |
| Software, algorithm |
mdtraj |
PMID:26488642
|
|
Analyzing MD data |
| Software, algorithm |
VMD |
PMID:8744570
|
RRID:SCR_001820
|
Analyzing MD data |
