3tx8 | pdb_00003tx8

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

spinqualitylabelsall models 3tx8, resolution 2.97Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3tx8 is a 1 chain structure with sequence from "micrococcus_glutamicus"_kinoshita_et_al._1958 "micrococcus glutamicus" kinoshita et al. 1958. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CL, PO4 NonStd Res: MSE Gene: dapE, Cgl1109, cg1260 ("Micrococcus glutamicus" Kinoshita et al. 1958) Activity: Succinyl-diaminopimelate desuccinylase, with EC number 3.5.1.18 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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 approximately 3 A 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. 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.,Brunger AT, Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams PD, Levitt M, Schroder GF Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):391-403. Epub 2012 Mar 16. PMID:22505259 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Proteopedia Page Contributors and Editors (what is this?)

OCA