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

BrungerA.T.; DasD.; DeaconA.M.GrantJ.TerwilligerT.C.ReadR.J.AdamsP.D.LevittM.Schr?derG.F.

首页> 外文期刊>Acta crystallographica.Section D. Biological crystallography >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

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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

机译：窝细化和自动化的应用模型构建一种困难的情况molecular-replacement定相:的结构假定的succinyl-diaminopimelate desuccinylase从棒状杆菌glutamicum

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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 ? 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.

机译：逐步由分子置换仍然困难的目标搜索模型或远离在水晶期刊的情况下弱或低分辨率。确定和细化的结构假定的succinyl-diaminopimelate Cgl1109从棒状杆菌desuccinylase glutamicum,3 ？同源建模的缔造者,molecular-replacement逐步移相器,网络(穴)细化和可变形的弹性自动使用自动构建的模型建立半自动方式,其次是决赛与凤凰优化循环。这个困难molecular-replacement案例说明了包括窝限制的力量源自一个起始模型指导在改进的运动模型。提供更好的生成的改进模型阶段起点自动构建和模型产生更多的显著差异的山峰傅里叶地图定位异常差异反常散射比标准细化。目前自动化程序的限制需要手动调整当地的序列同源模型和之间的失调目标序列。

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《Acta crystallographica.Section D. Biological crystallography》 |2012年第4期|391-403|共13页
作者
BrungerA.T.; DasD.; DeaconA.M.GrantJ.TerwilligerT.C.ReadR.J.AdamsP.D.LevittM.Schr?derG.F.;
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Los Alamos National Laboratory, United States;

Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research;

Department of Structural Biology, Stanford University, School of Medicine, United StatesDepartment of Bioengineering, University of California at Berkeley, Lawrence Berkeley NationalJoint Center for Structural Genomics, United States, Stanford Synchrotron Radiation LightsourceDept. of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and Photon ScienceJoint Center for Structural Genomics, United States, Protein Sciences Department, GenomicsInstitute of Complex Systems (ICS-6), Forschungszentrum, Jülich, Germany;

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正文语种英语
中图分类化学;
关键词
Corynebacterium glutamicum; Phase; RefiningAutomationcurrent limiting;

机译：棒状杆菌属glutamicum;阶段;RefiningAutomationcurrent限制;

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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

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