Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Escherichia coli) | DSBD | DSBD_ECOLI | UniprotID P36655 | |
| Strain, strain background (Escherichia coli) | BL21(DE3) | Stratagene | Competent cells | |
| Recombinant DNA reagent | pDzn3 | DOIs:10.1007/s12104-011-9347-9 and 10.1074/jbc.M805963200 | N-terminal domain of DsbD (nDsbD) (L2-V132) | Plasmid for wild-type nDsbD expression |
| Recombinant DNA reagent | pDzn8 | This study. | nDsbD (L2-V132) with residues H66-K73 replaced by AGG | Plasmid for Δ-loop nDsbD expression |
| Sequence-based reagent | Δ-loop nDsbD | This study. Synthesized by Sigma Aldrich. | PCR primer (forward): 5′-(AGGAAGCGAGATTTACCGCGATCGGCTG)−3′ | |
| Sequence-based reagent | Δ-loop nDsbD | This study. Synthesized by Sigma Aldrich. | PCR primer (reverse): 5′-(CCGGCCCAGACGCCTTGCGGCAGCTGC)−3′ | |
| Peptide, recombinant protein | Wild-type nDsbd | DOIs:10.1007/s12104-011-9347-9 and 10.1074/jbc.M805963200 | N-terminal domain of DsbD (nDsbD) (L2-V132) | Purified using a thrombin-cleavable C-terminal poly-His tag |
| Peptide, recombinant protein | Δ-loop nDsbd | This study. | nDsbD (L2-V132) with residues H66-K73 replaced by AGG | Purified using a thrombin-cleavable C-terminal poly-His tag |
| Commercial assay or kit | Sigma Thrombin CleanCleave Kit | Sigma-Aldrich | Used for removal of the poly-His tag | |
| Chemical compound, drug | KOD Hot Start DNA polymerase | Novagen | Used for PCR | |
| Chemical compound, drug | Pf1 phage | ASLA Biotech AB | Used for partial alignment for RDC measurements | |
| Software, algorithm | NMRPipe | DOI:10.1007/BF00197809 | Processing of NMR data | |
| Software, algorithm | CCPN Analysis (version 2.4.2) | DOI:10.1002/prot.20449 | RRID:SCR_016984 | Analysis of NMR spectra |
| Software, algorithm | CATIA | DOIs:10.1073/pnas.0804221105 and 10.1016/j.jmb.2011.07.017 and 10.1038/s41467-019-08557-8 | https://www.ucl.ac.uk/hansen-lab/catia/ | Global fitting of relaxation dispersion NMR data |
| Software, algorithm | GROMACS 4.5 | DOI:10.1002/jcc.20291 | RRID:SCR_014565 | Used for MD simulations |
| Software, algorithm | WHAT-IF | DOI:10.1093/nar/gkq453 | https://swift.cmbi.umcn.nl/whatif | Used to add missing atoms prior to MD simulations |
| Software, algorithm | Visual Molecular Dynamics (VMD) | DOI:10.1016/0263-7855(96)00018-5 | RRID:SCR_001820 | Used for analysis of distances, angles, hydrogen bonds in MD simulations and for rendering protein structures |
| Software, algorithm | MDAnalysis Python Library | DOI:10.1002/jcc.21787 | Used for analysis of distances, angles, hydrogen bonds in MD simulations | |
| Software, algorithm | blast 2.2.28+ (blastp) |
NCBI | RRID:SCR_001010
https://blast.ncbi.nlm.nih.gov/Blast.cgi |
Used to search for DsbD protein homologs |
| Software, algorithm | fasttree 2.1.7 | DOI:10.1371/journal.pone.0009490 | RRID:SCR_015501 | Used for building a phylogenetic tree |
| Software, algorithm | muscle 3.8.31 | DOI:10.1093/nar/gkh340 | RRID:SCR_011812 | Used for sequence alignment |
| Software, algorithm | Pymol Version 2.3.5 | Schrodinger, LLC | RRID:SCR_000305 | Used for rendering protein structural figures |
| Software, algorithm | Denzo/ Scalepack |
DOI:10.1016/S0076-6879(97)76066-X | Used for processing and scaling of X-ray data | |
| Software, algorithm | MOLREP | DOI: 10.1107/S0907444996012255 | Used for molecular replacement in solving X-ray structure | |
| Software, algorithm | Phenix.refine | DOI:10.1107/S09074444909052925 | RRID:SCR_016736 | Used for refinement of X-ray structure |
| Software, algorithm | Coot | DOI:10.1107/S0907444910007493 | RRID:SCR_014222 | Used for manual fitting of electron density in X-ray structure |