SIMBAD : a sequence-independent molecular-replacement pipeline

DOI: 10.1107/S2059798318005752

Authors: Adam J. Simpkin (University of Liverpool; Synchrotron SOLEIL) , Felix Simkovic (University of Liverpool) , Jens M. H. Thomas (University of Liverpool) , Martin Savko (Synchrotron Soleil) , Andrey Lebedev (STFC; CCP4, Research Complex at Harwell) , Ville Uski (STFC; CCP4, Research Complex at Harwell) , Charles Ballard (STFC; CCP4, Research Complex at Harwell) , Marcin Wojdyr (STFC; CCP4, Research Complex at Harwell; Global Phasing Ltd) , Rui Wu (Feil Family Brain and Mind Institute, Weill Cornell Medicine) , Ruslan Sanishvili (The Advanced Photon Source) , Yibin Xu (Walter and Eliza Hall Institute of Medical Research; University of Melbourne) , María-natalia Lisa (Institut Pasteur de Montevideo) , Alejandro Buschiazzo (Institut Pasteur de Montevideo) , William Shepard (Synchrotron Soleil) , Daniel J. Rigden (University of Liverpool) , Ronan M. Keegan (University of Liverpool; STFC; CCP4, Research Complex at Harwell)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Acta Crystallographica Section D Structural Biology , VOL 74

State: Published (Approved)
Published: July 2018
Diamond Proposal Number(s): 15945

Abstract: The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here, SIMBAD, a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD, this approach has solved novel cases that have otherwise proved difficult to solve.

Journal Keywords: molecular replacement pipeline; SIMBAD; contaminant; lattice search; structure solution

Subject Areas: Technique Development, Biology and Bio-materials, Information and Communication Technology


Instruments: I04-Macromolecular Crystallography

Documents:
rr5159.pdf