3TX8

Crystal structure of a succinyl-diaminopimelate desuccinylase (ArgE) from Corynebacterium glutamicum ATCC 13032 at 2.97 A resolution

Summary for 3TX8

• Entry DOI: 10.2210/pdb3tx8/pdb
• Descriptor: Succinyl-diaminopimelate desuccinylase, PHOSPHATE ION, CHLORIDE ION (3 entities in total)
• Functional Keywords: peptidase, structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi-biology, hydrolase
• Biological source: Corynebacterium glutamicum
• Total number of polymer chains: 1
• Total formula weight: 40401.61

Authors

Joint Center for Structural Genomics (JCSG),Brunger, A.T.,Terwilliger, T.C.,Read, R.J.,Adams, P.D.,Levitt, M.,Schroder, G.F. (deposition date: 2011-09-22, release date: 2011-10-26, Last modification date: 2024-11-27)

Primary citation

Brunger, A.T.,Das, D.,Deacon, A.M.,Grant, J.,Terwilliger, T.C.,Read, R.J.,Adams, P.D.,Levitt, M.,Schroder, G.F.
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.
Acta Crystallogr.,Sect.D, 68:391-403, 2012

PubMed 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.

PubMed: 22505259
DOI: 10.1107/S090744491104978X

Experimental method

X-RAY DIFFRACTION (2.972 Å)