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 <i>Corynebacterium glutamicum</i>

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.

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Affiliated Institutions

• Stanford Synchrotron Radiation Lightsource US
• Joint Center for Structural Genomics US
• Los Alamos National Laboratory US
• Lawrence Berkeley National Laboratory US
• Forschungszentrum Jülich DE
• Howard Hughes Medical Institute US
• Stanford University US
• University of Cambridge GB
• SLAC National Accelerator Laboratory US
• Genomics Institute of the Novartis Research Foundation US

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