<i>SnB</i>version 2.3: triplet sieve phasing for centrosymmetric structures

Xu, Hong‐Liang; Smith, A.B.; Sahinidis, Nikolaos V.; Weeks, Charles M.

doi:10.1107/s0021889808007966

Cited by 5 publications

(3 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The diffraction data were processed using the HKL2000 program suite (HKL Research). The heavy atom sites were identified with the program SnB 30 . The experimental phases were calculated using the program AutoSHARP 31 .…”

Section: Data Collection and Structure Determinationmentioning

confidence: 99%

Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Tanaka

Hipolito

Maturana

et al. 2013

Nature

232

287

View full text Add to dashboard Cite

Multidrug and toxic compound extrusion (MATE) family transporters are conserved in the three primary domains of life (Archaea, Bacteria and Eukarya), and export xenobiotics using an electrochemical gradient of H(+) or Na(+) across the membrane. MATE transporters confer multidrug resistance to bacterial pathogens and cancer cells, thus causing critical reductions in the therapeutic efficacies of antibiotics and anti-cancer drugs, respectively. Therefore, the development of MATE inhibitors has long been awaited in the field of clinical medicine. Here we present the crystal structures of the H(+)-driven MATE transporter from Pyrococcus furiosus in two distinct apo-form conformations, and in complexes with a derivative of the antibacterial drug norfloxacin and three in vitro selected thioether-macrocyclic peptides, at 2.1-3.0 Å resolutions. The structures, combined with functional analyses, show that the protonation of Asp 41 on the amino (N)-terminal lobe induces the bending of TM1, which in turn collapses the N-lobe cavity, thereby extruding the substrate drug to the extracellular space. Moreover, the macrocyclic peptides bind the central cleft in distinct manners, which correlate with their inhibitory activities. The strongest inhibitory peptide that occupies the N-lobe cavity may pave the way towards the development of efficient inhibitors against MATE transporters.

show abstract

Section: Data Collection and Structure Determinationmentioning

confidence: 99%

Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Tanaka

Hipolito

Maturana

et al. 2013

Nature

232

287

View full text Add to dashboard Cite

show abstract

“…One feature of using selenomethionine is that, depending on the protein and the size of the unit cell, a particular system may have very large numbers of heavy atoms that must be located in the course of phasing. In general this can be a major hurdle, although in favourable cases the power of direct methods [SHELXD (Schneider & Sheldrick, 2002), SnB (Xu et al, 2008) and HySS (Grosse-Kunstleve & Adams, 2003)], combined with the fact that the Se atoms are typically well ordered, has led to very large systems being solved, e.g. 160 selenium sites for ketopantoate hydroxymethyltransferase from E. coli, which crystallized with two decamers in the asymmetric unit (von Delft et al, 2003).…”

Section: Substitution Of Selenomethionine For Methioninementioning

confidence: 99%

An overview of heavy-atom derivatization of protein crystals

Pike

Garman

Krojer

et al. 2016

Acta Crystallogr D Struct Biol

View full text Add to dashboard Cite

Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in lowresolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.

show abstract

“…Models and algorithms have been developed for centrosymmetric and non-centrosymmetric structures. For the former case, these developments have already led to software that is distributed to practitioners of crystallography (Xu et al, 2008). …”

Section: Structure Determination From Single-crystal X-ray Diffractmentioning

confidence: 99%

Optimization techniques in molecular structure and function elucidation

Sahinidis

2009

Computers & Chemical Engineering

Self Cite

View full text Add to dashboard Cite

This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems.

show abstract

SnBversion 2.3: triplet sieve phasing for centrosymmetric structures

Cited by 5 publications

References 11 publications

Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

An overview of heavy-atom derivatization of protein crystals

Optimization techniques in molecular structure and function elucidation

Contact Info

Product

Resources

About