Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum
Year: 2012
Type: article
Abstract: Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.
Institutions: Howard Hughes Medical Institute, Stanford University, SLAC National Accelerator Laboratory, Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Genomics Institute of the Novartis Research Foundation, Los Alamos National Laboratory, University of Cambridge, Lawrence Berkeley National Laboratory, University of California, Berkeley, Stanford Medicine, Forschungszentrum Jülich
Language: English
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $4,740
Funders: Howard Hughes Medical Institute, U.S. Department of Energy, Wellcome Trust, National Institutes of Health, National Institute of General Medical Sciences, National Center for Research Resources, Basic Energy Sciences, Biological and Environmental Research, Lawrence Berkeley National Laboratory, SLAC National Accelerator Laboratory
Awards: Phenix: Integrated algorithms for high quality models from crystallographic and cryo-EM data, Joint Center for Structural Genomics, G1398330795, G1614572836, G1643223109, G193590374, G2807428303, G301008592, G3444594369, G4047395780, Protein crystallography: development of new methods, and application to the study of pathogenesis., Joint Center for Structural Genomics (JCSG-2), Accurate Modeling in Structural Genomics, G7444770027, G8346220699, Protein crystallography: development of new methods, and application to the study of pathogenesis., G9000331358
OpenAlex ID: W2115813898