Mathematical aspects of molecular replacement. IV. Measure-theoretic decompositions of motion spaces

被引:4
作者
Chirikjian, Gregory S. [1 ]
Sajjadi, Sajdeh [1 ]
Shiffman, Bernard [2 ]
Zucker, Steven M. [2 ]
机构
[1] Johns Hopkins Univ, Dept Mech Engn, 3400 N Charles St, Baltimore, MD 21218 USA
[2] Johns Hopkins Univ, Dept Math, 3400 N Charles St, Baltimore, MD 21218 USA
来源
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES | 2017年 / 73卷
基金
美国国家科学基金会;
关键词
fundamental domain; molecular replacement; measure theory; coset space; discrete subgroup; BILBAO CRYSTALLOGRAPHIC SERVER; PROTEIN DATA-BANK; UNITS;
D O I
10.1107/S2053273317007227
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
In molecular-replacement (MR) searches, spaces of motions are explored for determining the appropriate placement of rigid-body models of macromolecules in crystallographic asymmetric units. The properties of the space of non-redundant motions in an MR search, called a 'motion space', are the subject of this series of papers. This paper, the fourth in the series, builds on the others by showing that when the space group of a macromolecular crystal can be decomposed into a product of two space subgroups that share only the lattice translation group, the decomposition of the group provides different decompositions of the corresponding motion spaces. Then an MR search can be implemented by trading off between regions of the translation and rotation subspaces. The results of this paper constrain the allowable shapes and sizes of these subspaces. Special choices result when the space group is decomposed into a product of a normal Bieberbach subgroup and a symmorphic subgroup (which is a common occurrence in the space groups encountered in protein crystal-lography). Examples of Sohncke space groups are used to illustrate the general theory in the three-dimensional case (which is the relevant case for MR), but the general theory in this paper applies to any dimension.
引用
收藏
页码:387 / 402
页数:16
相关论文
共 27 条
  • [1] [Anonymous], 1990, Crystalline symmetries: An informal mathematical introduction
  • [2] [Anonymous], 1987, Classical tessellations and three-manifolds
  • [3] Aroyo MI, 2011, BULG CHEM COMMUN, V43, P183
  • [4] Bilbao crystallographic server: I. Databases and crystallographic computing programs
    Aroyo, MI
    Perez-Mato, JM
    Capillas, C
    Kroumova, E
    Ivantchev, S
    Madariaga, G
    Kirov, A
    Wondratschek, H
    [J]. ZEITSCHRIFT FUR KRISTALLOGRAPHIE, 2006, 221 (01): : 15 - 27
  • [5] The Protein Data Bank
    Berman, HM
    Battistuz, T
    Bhat, TN
    Bluhm, WF
    Bourne, PE
    Burkhardt, K
    Iype, L
    Jain, S
    Fagan, P
    Marvin, J
    Padilla, D
    Ravichandran, V
    Schneider, B
    Thanki, N
    Weissig, H
    Westbrook, JD
    Zardecki, C
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2002, 58 : 899 - 907
  • [6] Boisen M., 1990, MATH CRYSTALLOGRAPHY, V15
  • [7] Burns G., 2013, Space Groups for Solid State Scientists
  • [8] Charlap L.S., 1986, Bieberbach groups and flat manifolds
  • [9] Mathematical aspects of molecular replacement. III. Properties of space groups preferred by proteins in the Protein Data Bank
    Chirikjian, G.
    Sajjadi, S.
    Toptygin, D.
    Yan, Y.
    [J]. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2015, 71 : 186 - 194
  • [10] Collision-free configuration-spaces in macromolecular crystals
    Chirikjian, Gregory S.
    Shiffman, Bernard
    [J]. ROBOTICA, 2016, 34 (08) : 1679 - 1704