Combining direct methods with isomorphous replacement or anomalous scattering data. VIII. Phasing experimental SIR data with the replacing atoms in a centrosymmetric arrangement

Liu, Yudong; Gu, Yizhou; Zheng, Chao; Hao, Quan; Fan, Hong-Yi

doi:10.1107/s0907444998017703

Cited by 5 publications

(5 citation statements)

References 13 publications

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“…Similar investigations were reported by different authors during 1960s and 1970s 33–38. From the early 1980s to the early 2000s, the combination of direct methods with SAD/SIR data was emphasized in direct‐method research worldwide 39–63. The first application of direct‐method SAD phasing in solving originally unknown protein structures was reported in 1999 56 with data at 2.1 Å resolution.…”

Section: Direct Methods In Macromolecular Crystallographysupporting

confidence: 67%

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Direct methods beyond small‐molecule crystallography

Fan

2010

Physica Status Solidi (a)

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The development of direct methods outside their traditional field began since the middle 1960s. New applications were explored gradually in four directions. They are the transition of: (i) from single crystals to powder samples, (ii) from X‐ray crystallography to electron microscopy (EM), (iii) from periodic structures to incommensurate structures and (iv) from small molecules to macromolecular structures. The research on methods of solving crystal structures at the Institute of Physics in Beijing has been focused on the last three directions. The transition of direct methods from X‐ray crystallography to EM led to a two‐step image processing technique in high‐resolution electron microscopy (HREM). This technique combines information of EM and that of electron diffraction (ED) revealing the structure of minute crystals that are unsuitable for X‐ray diffraction analysis. The transition of direct methods from periodic crystal structures to incommensurate structures led to the multi‐dimensional direct methods enabling ab initio solution of incommensurate modulated structures and composite structures without relying on an assumed modulation model or even the known basic structure. Finally the combination of direct methods with traditional protein crystallographic methods has greatly enhanced the ability of solving protein structures.

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Section: Direct Methods In Macromolecular Crystallographysupporting

confidence: 67%

“…The test on Hg‐derivative SIR data 55 showed that, owing to the centric arrangement of the Hg‐substructure, conventional SIR phasing methods failed to break the phase ambiguity. However, direct‐method SIR phasing followed by density modification produced an acceptable result (see Fig.…”

Section: Direct Methods In Macromolecular Crystallographymentioning

confidence: 99%

Direct methods beyond small‐molecule crystallography

Fan

2010

Physica Status Solidi (a)

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“…The structure of MKLN 1-205 was solved by sulfur SAD with the HySS (Hybrid Substructure Search) submodule of the Phenix package (Adams et al, 2002) together with the Oasis program of the CCP4 suite (Liu et al, 1999;Winn et al, 2011). The substructure was refined using SHARP (Bricogne et al, 2003), and iterations between automatically building partial models with the Buccaneer software (Cowtan, 2006) using the modified map and refinement of the partial model and density modification in SHARP finally led to an improved model, which was then completed manually and further refined using REFMAC (Skubak et al, 2004).…”

Section: Structure Solutionmentioning

confidence: 99%

The LisH Motif of Muskelin Is Crucial for Oligomerization and Governs Intracellular Localization

et al. 2015

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Graphical Abstract Highlights d The LisH motif of muskelin acts as a dimerization interface d The generic binding site in the discoidin domain mediates a head-to-tail interaction d Muskelin forms a tetramer as a dimer of dimers via both interfaces d An impaired LisH dimerization relocates muskelin from the cytoplasm to the nucleus In Brief Muskelin organizes the retrograde transport of certain GABA A receptors. In the crystal structure of the N-terminal discoidin domain and LisH motif, Delto et al. observe a LisH-mediated dimer. They demonstrate that this interaction is required for muskelin tetramerization and determines cellular localization of muskelin. Accession Numbers 4OYU Delto et al., 2015, Structure 23, 364-373 February 3, SUMMARYNeurons regulate the number of surface receptors by balancing the transport to and from the plasma membrane to adjust their signaling properties. The protein muskelin was recently identified as a key factor guiding the transport of a1 subunit-containing GABA A receptors. Here we present the crystal structure of muskelin, comprising its N-terminal discoidin domain and Lis1-homology (LisH) motif. The molecule crystallized as a dimer with the LisH motif exclusively mediating oligomerization. Our subsequent biochemical analyses confirmed that the LisH motif acts as a dimerization element in muskelin. Together with an intermolecular head-to-tail interaction, the LisH-dependent dimerization is required to assemble a muskelin tetramer. Intriguingly, our cellular studies revealed that the loss of this dimerization results in a complete redistribution of muskelin from the cytoplasm to the nucleus and impairs muskelin's function in GABA A receptor transport. These studies demonstrate that the LisH-dependent dimerization is a crucial factor for muskelin function.

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“…A direct method to resolve this ambiguity has been reported using experimental SIR data to 2.0 Ð resolution for the small protein avine pancreatic polypeptide (previous work on the method used synthetic ideal data). 106 A four-phase structure invariant (4PSI) can be derived from four pairs of equivalent re£ections from two isomorphous datasets; the probability distribution of 4PSIs can be derived by integration of direct methods with isomorphous replacement and their reliability was shown to be comparable with that for 3PSIs. 107…”

Section: Heavy Atom Methodsmentioning

confidence: 99%

5 Molecular structure from X-ray diffraction

Powell

2000

Annu. Rep. Prog. Chem., Sect. C

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The last of these reports appeared four years ago; 1 a number of major advances in structure elucidation have appeared in laboratories in that period, mostly in the ¢eld of macromolecular structure determination. This is largely because sub-100 non-hydrogen atom structure solution has become almost routine, with extremely robust solution and re¢nement programs being complemented by rapid data collection from single crystal samples. In many cases, the role of the in-house crystallographer in chemistry departments is to provide a service to synthetic chemists in an analogous way to that of NMR spectroscopists ¢fteen or twenty years ago. Many chemical crystallographers have used this as an opportunity to study more dif¢cult structures, for example larger molecules from both single crystal and powder methods, using twin datasets, and looking more closely at structures in charge density studies.This increased ease has not removed the perils of being ``Marshed''; the well-known investigator into errors in space group determination has examined structures deposited into the Cambridge Structural Database (CSD) with space group P1, of which more than 20% are incorrect. 2 The majority of errors appear to be due to typographical errors in the original publication, but a signi¢cant minority are due to incorrect space group assignment (usually authors missing a centre of inversion, and assigning P1 rather than P1, or not recognizing higher symmetry, e.g., assigning P1 (triclinic) rather than C2 (monoclinic). However, the author notes that in some cases of true P1 structures, the deviation from centrosymmetry is as small as 0.1 Ð, and would be expected to lead to dif¢culties in re¢nement unless the problem had been recognized, as the following example illustrates.The solution and re¢nement of the antibiotics Emycin E and D provides a warning not to abide by conventional wisdom under all circumstances. 3 Both antibiotics crystallize in a triclinic space group with two molecules in the asymmetric unit (Z 2). The dataset for Emycin E was in accordance with the normal measure of centricity, a mean hjE 2 À 1ji value of 0.978 (the expected value for a centrosymmetric dataset is 0.968, and is 0.736 for acentric), while that for Emycin D was 0.829. Both can be re¢ned to low residual indices (R-factors) in space group

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Combining direct methods with isomorphous replacement or anomalous scattering data. VIII. Phasing experimental SIR data with the replacing atoms in a centrosymmetric arrangement

Cited by 5 publications

References 13 publications

Direct methods beyond small‐molecule crystallography

Direct methods beyond small‐molecule crystallography

The LisH Motif of Muskelin Is Crucial for Oligomerization and Governs Intracellular Localization

5 Molecular structure from X-ray diffraction

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