http://chineseinput.net/에서 pinyin(병음)방식으로 중국어를 변환할 수 있습니다.
변환된 중국어를 복사하여 사용하시면 됩니다.
Experimental phasing using zinc anomalous scattering
Cha, Sun-Shin,An, Young Jun,Jeong, Chang-Sook,Kim, Min-Kyu,Lee, Sung-Gyu,Lee, Kwang-Hoon,Oh, Byung-Ha International Union of Crystallography 2012 Acta crystallographica. Section D, Biological crys Vol.68 No.9
<▼1><P>The surface of proteins can be charged with zinc ions and the anomalous signals from these zinc ions can be used for structure determination of proteins.</P></▼1><▼2><P>Zinc is a suitable metal for anomalous dispersion phasing methods in protein crystallography. Structure determination using zinc anomalous scattering has been almost exclusively limited to proteins with intrinsically bound zinc(s). Here, it is reported that multiple zinc ions can easily be charged onto the surface of proteins with no intrinsic zinc-binding site by using zinc-containing solutions. Zn derivatization of protein surfaces appears to be a largely unnoticed but promising method of protein structure determination.</P></▼2>
Lee, Sang Jae,Lee, Seung‐,Jae,Lee, Seung Kyu,Yoon, Hye‐,Jin,Lee, Hyung Ho,Kim, Kyeong Kyu,Lee, Bong Jin,Lee, Byung Il,Suh, Se Won International Union of Crystallography 2012 Acta crystallographica. Section D, Biological crys Vol.68 No.7
<P>Peptide deformylase (PDF) catalyzes the removal of the formyl group from the N‐terminal methionine residue in newly synthesized polypeptides, which is an essential process in bacteria. Four new inhibitors of PDF that belong to two different classes, hydroxamate/pseudopeptide compounds [PMT387 (7a) and PMT497] and reverse‐hydroxamate/nonpeptide compounds [PMT1039 (15e) and PMT1067], have been developed. These compounds inhibited the growth of several pathogens involved in respiratory‐tract infections, such as <I>Streptococcus pneumoniae</I>, <I>Moraxella catarrhalis</I> and <I>Haemophilus influenzae</I>, and leading nosocomial pathogens such as <I>Staphylococcus aureus</I> and <I>Klebsiella pneumoniae</I> with a minimum inhibitory concentration (MIC) in the range 0.1–0.8 mg ml<SUP>−1</SUP>. Interestingly, the reverse‐hydroxamate/nonpeptide compounds showed a 250‐fold higher antimicrobial activity towards <I>S.?aureus</I>, although the four compounds showed similar <I>K</I><SUB>i</SUB> values against <I>S.?aureus</I> PDF enzymes, with <I>K</I><SUB>i</SUB> values in the 11–85 n<I>M</I> range. To provide a structural basis for the discovery of additional PDF inhibitors, the crystal structures of <I>S. aureus</I> PDF in complex with the four inhibitors were determined at resolutions of 1.90–2.30 Å. The inhibitor‐bound structures displayed distinct deviations depending on the inhibitor class. The distance between the Zn<SUP>2+</SUP> ion and the carbonyl O atom of the hydroxamate inhibitors (or the hydroxyl O atom of the reverse‐hydroxamate inhibitors) appears to be correlated to <I>S.?aureus</I> inhibition activity. The structural information reported in this study should aid in the discovery of new PDF inhibitors that can be used as novel antibacterial drugs.</P>
Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects
Kim, Jeongho,Kim, Kyung Hwan,Lee, Jae Hyuk,Ihee, Hyotcherl International Union of Crystallography 2010 Acta crystallographica. Section A, Foundations of Vol.66 No.2
<P>In recent years, the time-resolved X-ray diffraction technique has been established as an excellent tool for studying reaction dynamics and protein structural transitions with the aid of 100 ps X-ray pulses generated from third-generation synchrotrons. The forthcoming advent of the X-ray free-electron laser (XFEL) will bring a substantial improvement in pulse duration, photon flux and coherence of X-ray pulses, making time-resolved X-ray diffraction even more powerful. This technical breakthrough is envisioned to revolutionize the field of reaction dynamics associated with time-resolved diffraction methods. Examples of candidates for the first femtosecond X-ray diffraction experiments using highly coherent sub-100 fs pulses generated from XFELs are presented in this paper. They include the chemical reactions of small molecules in the gas and solution phases, solvation dynamics and protein structural transitions. In these potential experiments, ultrafast reaction dynamics and motions of coherent rovibrational wave packets will be monitored in real time. In addition, high photon flux and coherence of XFEL-generated X-ray pulses give the prospect of single-molecule diffraction experiments.</P>
Pradhan, Subhashis,Moon, Dohyun,John, Rohith P. International Union of Crystallography 2016 Acta crystallographica. Section B, Structural scie Vol.72 No.1
<P>A supramolecular compound, <I>catena</I>‐poly{[Cu<SUB>2</SUB>(1,3‐μ<SUB>2</SUB>‐(1<I>a</I>))<SUB>2</SUB>(μ<SUB>2</SUB>‐ter)<SUB>2</SUB>(H<SUB>2</SUB>O)<SUB>2</SUB>]<SUB><I>n</I></SUB>·(6H<SUB>2</SUB>O)<SUB><I>n</I></SUB>} (1) has been synthesized using (1<I>a</I>) [(1<I>a</I> = <I>N</I><SUP>1</SUP>,<I>N</I><SUP>3</SUP>,<I>N</I><SUP>5</SUP>‐trimethyl‐<I>N</I><SUP>1</SUP>,<I>N</I><SUP>3</SUP>,<I>N</I><SUP>5</SUP>‐tris((pyridin‐4‐yl)methyl)‐1,3,5‐benzene tricarboxamide] and terephthalate (ter) as the pillaring unit by self‐assembly. The terephthalate units are connected by copper(II) ions forming a single strand, while a pair of such strands are then linked by (1<I>a</I>) <I>via</I> two pyridyl terminal arms bound to copper(II) nodes on either side forming a one‐dimensional double stranded assembly propagating along the <I>c</I> axis. The compound crystallizes in the <I>Fdd</I>2 space group. The cavity created in the interior of this double strand assembly trap six water molecules and are stabilized by hydrogen bonding with the host. The arrangement of the pair of acyclic water trimers in isolated cavities of (1) is such that it resembles a closed‐bracket‐like formation. The Hirshfeld surface analysis of (1) reveals the presence of strong intermolecular hydrogen‐bonding interactions between one‐dimensional ladder‐like units and with the water trimer in the host cavity. The copper(II)‐containing coordination polymer also acts as an efficient catalyst for the Glaser–Hay homo‐coupling reaction.</P>
Photolysis of Br<sub>2</sub>in CCl<sub>4</sub>studied by time-resolved X-ray scattering
Kong, Qingyu,Lee, Jae Hyuk,Lo Russo, Manuela,Kim, Tae Kyu,Lorenc, Maciej,Cammarata, Marco,Bratos, Savo,Buslaps, Thomas,Honkimaki, Veijo,Ihee, Hyotcherl,Wulff, Michael International Union of Crystallography 2010 Acta crystallographica. Section A, Foundations of Vol.66 No.2
<P>A time-resolved X-ray solution scattering study of bromine molecules in CCl4is presented as an example of how to track atomic motions in a simple chemical reaction. The structures of the photoproducts are tracked during the recombination process, geminate and non-geminate, from 100 ps to 10 µs after dissociation. The relaxation of hot Br2<SUP>*</SUP>molecules heats the solvent. At early times, from 0.1 to 10 ns, an adiabatic temperature rise is observed, which leads to a pressure gradient that forces the sample to expand. The expansion starts after about 10 ns with the laser beam sizes used here. When thermal artefacts are removed by suitable scaling of the transient solvent response, the excited-state solute structures can be obtained with high fidelity. The analysis shows that 30% of Br2<SUP>*</SUP>molecules recombine directly along the<I>X</I>potential, 60% are trapped in the<I>A</I>/<I>A</I>′ state with a lifetime of 5.5 ns, and 10% recombine non-geminately<I>via</I>diffusive motion in about 25 ns. The Br-Br distance distribution in the<I>A</I>/<I>A</I>′ state peaks at 3.0 Å.</P>
Lee, Tae-Ho,Kim, Sung-Joon,Shin, Eunjoo,Takaki, Setsuo International Union of Crystallography 2006 Acta crystallographica. Section B, Structural scie Vol.62 No.6
<P>The ordered structure of Cr2N precipitates in high-nitrogen austenitic steel was investigated utilizing high-resolution neutron powder diffractometry (HRPD). On the basis of the Rietveld refinement of neutron diffraction patterns, the ordered Cr2N superstructure was confirmed to be trigonal (space group P\overline 3 1m), with lattice parameters <I>a</I> = 4.800 (4) and <I>c</I> = 4.472 (5) Å, as suggested in previous transmission electron microscopy studies [Lee, Oh, Han, Lee, Kim & Takaki (2005). <I>Acta Cryst</I>. B61, 137-144; Lee, Kim & Takaki (2006). <I>Acta Cryst</I>. B62, 190-196]. The occupancies of the N atoms in four crystallographic sites [1(<I>a</I>), 1(<I>b</I>), 2(<I>d</I>) and 2(<I>c</I>) Wyckoff sites] were determined to be 1.00 (5), 0.0, 0.74 (9) and 0.12 (3), respectively, reflecting a partial disordering of N atoms along the <I>c</I> axis. The position of the metal atom was specified to be <I>x</I> = 0.346 (8) and <I>z</I> = 0.244 (6), corresponding to a deviation from the ideal position (<I>x</I> = 0.333 and <I>z</I> = 0.250). This deviation caused the (\,{1 \over 3}{1 \over 3}0)-type superlattice reflection to appear. A comparison between the ideal and measured crystal structures of Cr2N was performed using a computer simulation of selected-area diffraction patterns.</P>
Ichiyanagi, K.,Sato, T.,Nozawa, S.,Kim, K. H.,Lee, J. H.,Choi, J.,Tomita, A.,Ichikawa, H.,Adachi, S.,Ihee, H.,Koshihara, S. International Union of Crystallography 2009 Journal of synchrotron radiation Vol.16 No.3
<▼1><P>A new method of time-resolved solution scattering utilizing X-ray multilayer optics is presented.</P></▼1><▼2><P>100 ps time-resolved X-ray solution-scattering capabilities have been developed using multilayer optics at the beamline NW14A, Photon Factory Advanced Ring, KEK. X-ray pulses with an energy bandwidth of Δ<I>E</I>/<I>E</I> = 1–5% are generated by reflecting X-ray pulses (Δ<I>E</I>/<I>E</I> = 15%) through multilayer optics, made of W/B<SUB>4</SUB>C or depth-graded Ru/C on silicon substrate. This tailor-made wide-bandwidth X-ray pulse provides high-quality solution-scattering data for obtaining photo-induced molecular reaction dynamics. The time-resolved solution scattering of CH<SUB>2</SUB>I<SUB>2</SUB> in methanol is demonstrated as a typical example.</P></▼2>
Structures of the γ‐class carbonic anhydrase homologue YrdA suggest a possible allosteric switch
Park, Hye‐,Mi,Park, Jeong‐,Hoh,Choi, Ji‐,Woo,Lee, Jieun,Kim, Bo Yeon,Jung, Che‐,Hun,Kim, Jeong‐,Sun International Union of Crystallography 2012 Acta crystallographica. Section D, Biological crys Vol.68 No.8
<P>The YrdA protein shows high sequence similarity to γ‐class carbonic anhydrase (γ‐CA) proteins and is classified as part of the γ‐CA protein family. However, its function has not been fully elucidated as it lacks several of the conserved residues that are considered to be necessary for γ‐CA catalysis. Interestingly, a homologue of γ‐CA from <I>Methanosarcina thermophila</I> and a β‐carboxysomal γ‐CA from a β‐cyanobacterium have shown that these catalytic residues are not always conserved in γ‐CAs. The crystal structure of YrdA from <I>Escherichia coli</I> (ecYrdA) is reported here in two crystallographic forms. The overall structure of ecYrdA is also similar to those of the γ‐CAs. One loop around the putative catalytic site shows a number of alternative conformations. A His residue (His70) on this loop coordinates with, or is reoriented from, the catalytic Zn<SUP>2+</SUP> ion; this is similar to the conformations mediated by an Asp residue on the catalytic loops of β‐CA proteins. One Trp residue (Trp171) also adopts two alternative conformations that may be related to the spatial positions of the catalytic loop. Even though significant CA activity could not be detected using purified ecYrdA, these structural features have potential functional implications for γ‐CA‐related proteins.</P>