scholarly journals Crystallographic studies of the extracytoplasmic function σ factor σJfromMycobacterium tuberculosis

2015 ◽  
Vol 71 (8) ◽  
pp. 946-950 ◽  
Author(s):  
Kapil Goutam ◽  
Arvind Kumar Gupta ◽  
Balasubramanian Gopal
Keyword(s):  
Oxidative Stress ◽  
Cellular Response ◽  
European Synchrotron Radiation Facility ◽  
Human Macrophage ◽  
Late Stationary Phase ◽  
Macrophage Infection ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
C Terminus ◽  
Σ Factor

Mycobacterium tuberculosishas multiple σ factors which enable the bacterium to reprogram its transcriptional machinery under diverse environmental conditions. σJ, an extracytoplasmic function σ factor, is upregulated in late stationary phase cultures and during human macrophage infection. σJgoverns the cellular response to hydrogen peroxide-mediated oxidative stress. σJdiffers from other canonical σ factors owing to the presence of a SnoaL_2 domain at the C-terminus. σJcrystals belonged to the tetragonal space groupI422, with unit-cell parametersa=b= 133.85,c= 75.08 Å. Diffraction data were collected to 2.16 Å resolution on the BM14 beamline at the European Synchrotron Radiation Facility (ESRF).

scholarly journals Cloning, expression, purification, crystallization and preliminary crystallographic analysis of the C-terminal domain of Par-4 (PAWR)

2014 ◽  
Vol 70 (9) ◽  
pp. 1224-1227 ◽  
Author(s):  
Udaya Kumar Tiruttani Subhramanyam ◽  
Jan Kubicek ◽  
Ulf B. Eidhoff ◽  
Joerg Labahn
Keyword(s):  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Intrinsically Disordered ◽  
Tumour Suppressor Function ◽  
C Terminus ◽  
Apoptotic Protein

Prostate apoptosis response-4 protein is an intrinsically disordered pro-apoptotic protein with tumour suppressor function. Par-4 is known for its selective induction of apoptosis in cancer cells only and its ability to interact with various apoptotic proteinsviaits C-terminus. Par-4, with its unique function and various interacting partners, has gained importance as a potential target for cancer therapy. The C-terminus of the rat homologue of Par-4 was crystallized and a 3.7 Å resolution X-ray diffraction data set was collected. Preliminary data analysis shows the space group to beP41212. The unit-cell parameters area=b= 115.351,c= 123.663 Å, α = β = γ = 90°.

scholarly journals Characterization, crystallization and preliminary X-ray crystallographic analysis of the human Uba5 C-terminus–Ufc1 complex

2014 ◽  
Vol 70 (8) ◽  
pp. 1093-1097 ◽  
Author(s):  
Shutao Xie
Keyword(s):  
Fusion Protein ◽  
Protein Molecule ◽  
Crystallographic Analysis ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Solution Crystallization ◽  
C Terminus ◽  
Peg 4000 ◽  
Minimal Region

Human Uba5, which contains an adenylation domain and a C-terminal region, is the smallest ubiquitin-like molecule-activating enzyme. The mechanism through which the enzyme recognizes Ufc1 and catalyzes the formation of the Ufc1–Ufm1 complex remains unknown. In this study, Uba5 residues 364–404 were demonstrated to be necessary for the transthiolation of Ufm1 to Ufc1, and Uba5 381–404 was identified to be the minimal region for Ufc1 recognition. The fusion protein between Uba5 381–404 and Ufc1 was cloned, expressed and purified, and exists as a homodimer in solution. Crystallization was performed at 293 K using PEG 4000 as precipitant; the optimized crystals diffracted to 3.0 Å resolution and had unit-cell parametersa=b= 82.49,c= 62.47 Å, α = β = 90, γ = 120°. With one fusion-protein molecule in the asymmetric unit, the Matthews coefficient and solvent content were calculated to be 2.55 Å3 Da−1and 51.84%, respectively.

scholarly journals Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the extracellular olfactomedin domain of gliomedin

2014 ◽  
Vol 70 (11) ◽  
pp. 1536-1539 ◽  
Author(s):  
Huijong Han ◽  
Petri Kursula
Keyword(s):  
Cell System ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Essential Proteins ◽  
Voltage Gated Sodium Channels ◽  
C Terminus ◽  
Neuronal Plasma Membrane

Gliomedin (GLDN) is one of the essential proteins in the development of the nodes of Ranvier in the vertebrate peripheral nervous system. An olfactomedin (OLF) domain is located at the GLDN extracellular C-terminus and is involved in the accumulation of neuronal plasma membrane voltage-gated sodium channels in the nodes by interacting with neurofascin and NrCAM. No structures of OLF domains have previously been reported. Here, the crystallization of the rat GLDN OLF domain, which was expressed in an insect-cell system, is reported. The crystal diffracted to 1.55 Å resolution and belonged to space groupP21, with unit-cell parametersa= 37.5,b= 141.7,c= 46.0 Å, β = 110.6°, and had two molecules in the asymmetric unit.

Crystallization and preliminary X-ray analysis of Saccharomyces cerevisiae Ypd1p, a key intermediate in phosphorelay signal transduction

1999 ◽  
Vol 55 (6) ◽  
pp. 1219-1221 ◽  
Author(s):  
Myong Gyong Lee ◽  
Jae Young Lee ◽  
Hyun Kyu Song ◽  
Se Won Suh
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Signal Transduction ◽  
Room Temperature ◽  
Soluble Form ◽  
Response Regulators ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
C Terminus ◽  
Hybrid Histidine Kinase

Ypd1p, a 167-residue protein from Saccharomyces cerevisiae, plays a key role in osmosensing phosphorelay signal transduction. It forms part of a multistep phosphorelay system which also includes Sln1p hybrid histidine kinase and two response regulators, Ssk1p and Skn7p. It has been overexpressed in soluble form in Escherichia coli with a His6-tag at its C-terminus. The recombinant protein has been crystallized at room temperature using ammonium sulfate and lithium sulfate as precipitants. Native diffraction data have been collected to 2.3 Å using synchrotron radiation. The crystals are triclinic, belonging to the space group P1, with unit-cell parameters a = 65.78, b = 66.74, c  =  65.75 Å, α = 106.60, β = 106.48, γ = 115.53°. The asymmetric unit contains four molecules of the monomeric recombinant Ypd1p, with a corresponding Vm of 2.75 Å3 Da−1 and a solvent content of 55.3%.

Structure of a new neurotoxin from the scorpion Buthus martensii Karsch at 1.76 Å

2000 ◽  
Vol 56 (1) ◽  
pp. 25-33 ◽  
Author(s):  
Xiao-Lin He ◽  
Jun-Peng Deng ◽  
Miao Wang ◽  
Ying Zhang ◽  
Da-Cheng Wang
Keyword(s):  
Potential Surface ◽  
Peptide Bond ◽  
Terminal Segment ◽  
Crystallographic Analysis ◽  
Molecular Replacement ◽  
Unit Cell Parameters ◽  
High Resolution Data ◽  
Group Iii ◽  
Cell Parameters ◽  
C Terminus

A new neurotoxin BmK M2, toxic to both mammals and insects, with the strongest toxicity in the BmK toxin series, has been purified from the Chinese scorpion Buthus martensii Karsch and crystallized with MPD at pH 7.5. The crystals are orthorhombic, belonging to space group P212121, with unit-cell parameters a = 36.64, b = 36.95, c = 37.23 Å. The structure was solved by molecular replacement and refined to R = 0.186 for all reflections to a resolution of 1.76 Å. The whole sequence (64 residues) of BmK M2 was determined by crystallographic analysis based on high-resolution data and the homologous model of BmK M8. The refined BmK M2 structure shows a non-proline cis peptide bond between Pro9 and His10 which enables the C-terminal segment to adopt a conformation different to that of the weak toxin BmK M8. Recently, a mutation analysis had suggested that both the tenth residue and the C-terminus play key roles in receptor binding. Therefore, these features may be related to the binding selectivity of the group III α-like toxins. The charge changes of residues 8, 10, 18, 28, 55 and 59 from neutral or negative to positive or neutral, which leads to a positive electrostatic potential surface, may be responsible for the high toxicity of BmK M2.

scholarly journals Crystal structure of the novel haloalkane dehalogenases

2014 ◽  
Vol 70 (a1) ◽  
pp. C1678-C1678
Author(s):  
Katsiaryna Tratsiak ◽  
Tatyana Prudnikova ◽  
Ivana Drienovska ◽  
Lukas Chrast ◽  
Jiri Damborsky ◽  
...  
Keyword(s):  
Czech Republic ◽  
Sequence Similarity ◽  
European Synchrotron Radiation Facility ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
The Czech Republic ◽  
Space Group ◽  
Practical Applications ◽  
Cell Parameters

Haloalkane dehalogenases (EC 3.8.1.5; HLDs) are microbial enzymes with catalytic activity for the hydrolytic conversion of xenobiotic and highly toxic halogenated aliphatic compounds to the corresponding alcohols. Biodegradation, biosensing, biocatalysis and cellular imaging are potentially practical applications for the HLDs. Two newly isolated and purified psychrophilic haloalkane dehalogenases, exhibiting interesting catalytic properties, DpcA from Psychrobacter cryohalolentis K5 and DmxA from Marinobacter sp. ELB17, were used for the crystallization experiments and structure determination. Diffracted crystals of DpcA(left) and DmxA(right) (see figure, the scale bar -100μm) were refined up to the 1.05 Å and 1.45 Å resolutions, respectively. Diffraction data for DpcA were collected on beamline 14.2 at the BESSY II electron-storage ring (Helmholtz-Zentrum Berlin (HZB), Germany) and equipped with a Rayonics MX-225 CCD detector at the wavelengths of 0.978 Å, and for DmxA were collected using Pilatus 6M-F detector at the wavelengths of 0.972 Å on the beamline ID29, at the European Synchrotron Radiation Facility (ESRF) in Grenoble (France). Crystals of DpcA belonged to P21 space group with unit-cell parameters: a = 41.3, b = 79.4, c = 43.5 A °, α = β = 90.0, γ = 95.0 and contained 1 molecule in the asymmetric unit. Crystals of DmxA belonged to P212121 space group, with unit-cell parameters: a = 43.371, b = 78.343, c = 150.51; α = γ = β = 90.0 and contained 2 molecules in the asymmetric unit. The structures were solved by molecular replacement with MOLREP from the CCP4 software suite. The coordinates of Xanthobacter autotrophicus (PDB code: 1B6G; 40% sequence identities for 121 residues and 53% sequence similarity was used as search model for DpcA structure and for DmxA from Rhodococcus rhodochrous (PDB entry 4E46; 48% sequence identity for 142 residues and 63% sequence similarity). Belonging to the superfamily of α/β - hydrolases, according to the catalytic pentad, HLDs are subdivided onto the three subfamilies. DpcA belongs to the HLD - I: Asp- His - Asp + Trp - Trp and DmxA to the HLD – II: Asp - His - Glu + Asn - Trp. We thank M. Weiss and S. Pühringer (BESSY). This work is supported by the Grant Agency of the Czech Republic (P207/12/0775).Also by the Ministry of Education of the Czech Republic (CZ.1.05/2.1.00/01.0024 and CZ.1.05/2.1.00/01.0001). The support of the Academy of Sciences of the Czech Republic is acknowledged as well.

Kinematical and Dynamical CBED Pattern Models: Increasing the Accuracy of the Unit-Cell Parameter Measurements Based on CBED Patterns

1990 ◽  
Vol 48 (2) ◽  
pp. 540-541
Author(s):  
I.N. Yadhikov ◽  
S.K. Maksimov
Keyword(s):  
Reciprocal Lattice ◽  
Unit Cell ◽  
Reciprocal Lattice Vector ◽  
Unit Cell Parameters ◽  
Lattice Vector ◽  
Cell Parameters ◽  
Accuracy Of Measurements ◽  
The Difference ◽  
Image Position ◽  
Convergent Beam

Convergent beam electron diffraction (CBED) is widely used as a microanalysis tool. By the relative position of HOLZ-lines (Higher Order Laue Zone) in CBED-patterns one can determine the unit cell parameters with a high accuracy up to 0.1%. For this purpose, maps of HOLZ-lines are simulated with the help of a computer so that the best matching of maps with experimental CBED-pattern should be reached. In maps, HOLZ-lines are approximated, as a rule, by straight lines. The actual HOLZ-lines, however, are different from the straights. If we decrease accelerating voltage, the difference is increased and, thus, the accuracy of the unit cell parameters determination by the method becomes lower.To improve the accuracy of measurements it is necessary to give up the HOLZ-lines substitution by the straights. According to the kinematical theory a HOLZ-line is merely a fragment of ellipse arc described by the parametric equationwith arc corresponding to change of β parameter from -90° to +90°, wherevector, h - the distance between Laue zones, g - the value of the reciprocal lattice vector, g‖ - the value of the reciprocal lattice vector projection on zero Laue zone.

Sectioned rubisco crystals in TEM

1990 ◽  
Vol 48 (3) ◽  
pp. 664-665
Author(s):  
Gunnel Karlsson ◽  
Jan-Olov Bovin ◽  
Michael Bosma
Keyword(s):  
Plant Cell ◽  
Carbon Fixation ◽  
Unit Cell ◽  
Protein Crystals ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Photosynthetic Carbon Fixation ◽  
Photosynthetic Carbon

RuBisCO (D-ribulose-l,5-biphosphate carboxylase/oxygenase) is the most aboundant enzyme in the plant cell and it catalyses the key carboxylation reaction of photosynthetic carbon fixation, but also the competing oxygenase reaction of photorespiation. In vitro crystallized RuBisCO has been studied earlier but this investigation concerns in vivo existance of RuBisCO crystals in anthers and leaves ofsugarbeets. For the identification of in vivo protein crystals it is important to be able to determinethe unit cell of cytochemically identified crystals in the same image. In order to obtain the best combination of optimal contrast and resolution we have studied different staining and electron accelerating voltages. It is known that embedding and sectioning can cause deformation and obscure the unit cell parameters.

Three Dimensional Structure of UMo8O26: Ordering of U-Vacancies

2002 ◽  
Vol 718 ◽  
Author(s):  
N.D. Zakharov ◽  
P. Werner
Keyword(s):  
Low Temperatures ◽  
Driving Force ◽  
Three Dimensional ◽  
Solid State Reaction Method ◽  
Dimensional Structure ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Selected Area Electron Diffraction ◽  
Transmission Electron ◽  
Edx Microanalysis

AbstractThe structure and composition of UMo8O26 synthesized by solid state reaction method have been investigated by High Resolution Transmission Electron Microscopy (HRTEM), Selected Area Electron Diffraction, and EDX microanalysis. The ordering of U vacancies results in considerable enlargement of unit cell parameters: an=6.44 nm, bn=1.45 nm, cn=1.6 nm. It is build up of four layers piled up in c direction. Each following layer is shifted relative to previous one by vector bn/4. Eight hexagonal tunnels in each layer are filled by U atoms, while the eight others are vacant (V). Interaction between U cations and vacancies is driving force for ordering. The variation of stoichiometry can be a reason for appearance of incommensurate modulations in these crystals. It seems plausible that this structure might also exhibit superconductivity at low temperatures.

A Crystallographic Study of Bis[S-benzyl-5-bromo-2-oxoindolin-3-ylidenemethanehydrazonthioate] Disulfide Solvated with Dimethylsulfoxide

2012 ◽  
Vol 9 (2) ◽  
pp. 87
Author(s):  
Mohd Abdul Fatah Abdul Manan ◽  
M. Ibrahim M. Tahir ◽  
Karen A. Crouse ◽  
Fiona N.-F. How ◽  
David J. Watkin
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Site Occupancy ◽  
Unit Cell Parameters ◽  
Intermolecular Hydrogen Bonds ◽  
Triclinic Space Group ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Thiol Form

The crystal structure of the title compound has been determined. The compound crystallized in the triclinic space group P -1, Z = 2, V = 1839 .42( 18) A3 and unit cell parameters a= 11. 0460( 6) A, b = 13 .3180(7) A, c=13. 7321 (8) A, a = 80.659(3 )0, b = 69 .800(3 )0 and g = 77 .007 (2)0 with one disordered dimethylsulfoxide solvent molecule with the sulfur and oxygen atoms are distributed over two sites; S101/S102 [site occupancy factors: 0.6035/0.3965] and 0130/0131 [site occupancy factor 0.3965/0.6035]. The C22-S2 l and C 19-S20 bond distances of 1. 779(7) A and 1. 788(8) A indicate that both of the molecules are connected by the disulfide bond [S20-S21 2.055(2) A] in its thiol form. The crystal structure reveals that both of the 5-bromoisatin moieties are trans with respect to the [S21-S20 and CI 9-Nl 8] and [S20-S21 and C22-N23] bonds whereas the benzyl group from the dithiocarbazate are in the cis configuration with respect to [S21-S20 and C19-S44] and [S20-S21 and C22-S36] bonds. The crystal structure is further stabilized by intermolecular hydrogen bonds of N9-H35···O16 formed between the two molecules and N28-H281 ···O130, N28-H281 ···O131 and C4 l-H4 l l ···O 131 with the solvent molecule.

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