Crystallization and preliminary X-ray analysis of Thermotoga maritima ribosome recycling factor

1999 ◽  
Vol 55 (12) ◽  
pp. 2049-2050 ◽  
Author(s):  
Maria Selmer ◽  
Salam Al-Karadaghi ◽  
Go Hirokawa ◽  
Akira Kaji ◽  
Anders Liljas
Keyword(s):  
Protein Synthesis ◽  
Diffraction Data ◽  
Thermotoga Maritima ◽  
Asymmetric Unit ◽  
Ribosome Recycling Factor ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Fourth Step ◽  
Prokaryotic Protein

Thermotoga maritima ribosome recycling factor (RRF) is one of the proteins catalyzing the fourth step in prokaryotic protein synthesis, ribosome recycling. The RRF protein was crystallized with ammonium sulfate. Native diffraction data to 2.55 Å resolution were obtained at the MAX II synchrotron from a flash-frozen crystal at 100 K. The crystals belong to space group P41212 or P43212, with unit-cell parameters a = b = 47, c = 298 Å, and probably contain one monomer per asymmetric unit.

scholarly journals Purification, crystallization and preliminary crystallographic analysis of a 4-thiouridine synthetase–RNA complex

2013 ◽  
Vol 69 (4) ◽  
pp. 421-424 ◽  
Author(s):  
Peter-Thomas Naumann ◽  
Charles T. Lauhon ◽  
Ralf Ficner
Keyword(s):  
Diffraction Data ◽  
Thermotoga Maritima ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Dependent Modification ◽  
Rna Complex

The sulfurtransferase 4-thiouridine synthetase (ThiI) is involved in the ATP-dependent modification of U8 in tRNA. ThiI fromThermotoga maritimawas cloned, overexpressed and purified. A complex comprising ThiI and a truncated tRNA was prepared and crystallized, and X-ray diffraction data were collected to a resolution of 3.5 Å. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 102.9,b= 112.8,c= 132.8 Å.

scholarly journals Neutron crystallographic study of heterotrimeric glutamine amidotransferase CAB

2019 ◽  
Vol 75 (3) ◽  
pp. 193-196
Author(s):  
Long Li ◽  
Motoyasu Adachi ◽  
Jian Yu ◽  
Koji Kato ◽  
Akira Shinoda ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Active Sites ◽  
Neutron Diffraction Data ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Glutamine Amidotransferase

Heterotrimeric glutamine amidotransferase CAB (GatCAB) possesses an ammonia-self-sufficient mechanism in which ammonia is produced and used in the inner complex by GatA and GatB, respectively. The X-ray structure of GatCAB revealed that the two identified active sites of GatA and GatB are markedly distant, but are connected in the complex by a channel of 30 Å in length. In order to clarify whether ammonia is transferred through this channel in GatCAB by visualizing ammonia, neutron diffraction studies are indispensable. Here, GatCAB crystals were grown to approximate dimensions of 2.8 × 0.8 × 0.8 mm (a volume of 1.8 mm3) with the aid of a polymer using microseeding and macroseeding processes. Monochromatic neutron diffraction data were collected using the neutron single-crystal diffractometer BIODIFF at the Heinz Maier-Leibnitz Zentrum, Germany. The GatCAB crystals belonged to space group P212121, with unit-cell parameters a = 74.6, b = 94.5, c = 182.5 Å and with one GatCAB complex (molecular mass 119 kDa) in the asymmetric unit. This study represented a challenge in current neutron diffraction technology.

Crystal chemistry and nomenclature of fillowite-type phosphates

2021 ◽  
Vol 59 (4) ◽  
pp. 781-796
Author(s):  
Frédéric Hatert ◽  
Edward S. Grew ◽  
Pietro Vignola ◽  
Nicola Rotiroti ◽  
Fabrizio Nestola ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Divalent Cations ◽  
Complex Structure ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Cation Sites ◽  
Cation Distributions

ABSTRACT The crystal chemistries of five samples of minerals belonging to the fillowite group were structurally investigated: (A) fillowite from the Buranga pegmatite, Rwanda; (B) fillowite from the Kabira pegmatite, Uganda; (C) johnsomervilleite from Loch Quoich, Scotland; (D) johnsomervilleite from the Malpensata pegmatite, Italy; and (E) chladniite from the Sapucaia pegmatite, Minas Gerais, Brazil. Their crystal structures were refined in space group R (No. 148), using single-crystal X-ray diffraction data, to R1 values of (A) 3.79%, (B) 3.52%, (C) 4.14%, (D) 4.04%, and (E) 5.59%. Unit-cell parameters are: (A) a = 15.122(1), c = 43.258(4) Å; (B) a = 15.125(1), c = 43.198(3) Å; (C) a = 15.036(2), c = 42.972(9) Å; (D) a = 15.090(2), c = 43.050(9) Å; and (E) a = 15.1416(6), c = 43.123(2) Å. The asymmetric unit contains 15 cation sites with coordinations ranging from V to IX, as well as six P sites. The complex structure can be split into three types of chains running parallel to the c axis. These chains are composed of edge- and face-sharing polyhedra. Detailed cation distributions were determined for all five samples, and their comparison allowed us to establish the general formula A3BC11(PO4)9 for fillowite-type phosphates, where A represents the group of sites mainly occupied by Na, B the Ca sites, and C the sites containing the divalent cations Fe2+, Mn, and Mg. This formula was accepted by the CNMNC, and the four valid mineral species occurring in the fillowite group are fillowite (C = Mn), johnsomervilleite (C = Fe2+), chladniite (C = Mg), and galileiite (B and C = Fe2+). Stornesite-(Y) is discredited, since this mineral corresponds to Y-bearing chladniite.

Crystallization and preliminary crystallographic studies of ribosome recycling factor from Escherichia coli

2000 ◽  
Vol 56 (1) ◽  
pp. 84-85 ◽  
Author(s):  
Jungmin Yun ◽  
Wookhyun Kim ◽  
Sung Chul Ha ◽  
Soo-Hyun Eom ◽  
Se Won Suh ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Synthesis ◽  
Final Stage ◽  
Unit Cell ◽  
Ribosome Recycling Factor ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Peg 400

Ribosome recycling factor (RRF) catalyzes the disassembly of a termination complex during the final stage of protein synthesis. RRF from Escherichia coli has been crystallized with PEG 400 as precipitant at 287 K. The crystal belongs to the trigonal space group P3121 (or P3221), with unit-cell parameters a = b = 48.08, c = 141.67 Å. Native data were collected from a frozen crystal to a resolution of 3.0 Å on a Cu Kα rotating-anode X-ray source.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of 3-ketoacyl-CoA thiolase A1887 fromRalstonia eutrophaH16

2015 ◽  
Vol 71 (6) ◽  
pp. 758-762
Author(s):  
Jieun Kim ◽  
Kyung-Jin Kim
Keyword(s):  
Ralstonia Eutropha ◽  
Size Exclusion ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Exclusion Chromatography ◽  
Fourth Step

The gene product of A1887 fromRalstonia eutropha(ReH16_A1887) has been annotated as a 3-ketoacyl-CoA thiolase, an enzyme that catalyzes the fourth step of β-oxidation degradative pathways by converting 3-ketoacyl-CoA to acyl-CoA.ReH16_A1887 was overexpressed and purified to homogeneity by affinity and size-exclusion chromatography. The degradative thiolase activity of the purifiedReH16_A1887 was measured and enzyme-kinetic parameters for the protein were obtained, withKm,Vmaxandkcatvalues of 158 µM, 32 mM min−1and 5 × 106 s−1, respectively. TheReH16_A1887 protein was crystallized in 17% PEG 8K, 0.1 MHEPES pH 7.0 at 293 K and a complete data set was collected to 1.4 Å resolution. The crystal belonged to space groupP43212, with unit-cell parametersa=b= 129.52,c= 114.13 Å, α = β = γ = 90°. The asymmetric unit contained two molecules, with a solvent content of 58.9%.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of theS-adenosylhomocysteine hydrolase (SAHH) fromThermotoga maritima

2014 ◽  
Vol 70 (11) ◽  
pp. 1563-1565 ◽  
Author(s):  
Miao He ◽  
Yingying Zheng ◽  
Chun-Hsiang Huang ◽  
Guojun Qian ◽  
Xiansha Xiao ◽  
...  
Keyword(s):  
Initial Phase ◽  
Thermotoga Maritima ◽  
Diffusion Method ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Adenosylhomocysteine Hydrolase ◽  
X Ray ◽  
Cell Parameters

S-Adenosylhomocysteine hydrolase (SAHH) catalyzes the reversible conversion ofS-adenosylhomocysteine into adenosine and homocysteine. The SAHH fromThermotoga maritima(TmSAHH) was expressed inEscherichia coliand the recombinant protein was purified and crystallized.TmSAHH crystals belonging to space groupC2, with unit-cell parametersa= 106.3,b= 112.0,c= 164.9 Å, β = 103.5°, were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.85 Å resolution. Initial phase determination by molecular replacement clearly indicated that the crystal contains one homotetramer per asymmetric unit. Further refinement of the crystal structure is in progress.

Crystallization and preliminary X-ray diffraction studies of the catalytic core of acetyl xylan esterase from Trichoderma reesei

1998 ◽  
Vol 54 (3) ◽  
pp. 430-432 ◽  
Author(s):  
Nina Hakulinen ◽  
Maija Tenkanen ◽  
Juha Rouvinen
Keyword(s):  
Trichoderma Reesei ◽  
Diffraction Data ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Acetyl Xylan Esterase ◽  
Unit Cell Parameters ◽  
Catalytic Core ◽  
Triclinic Space Group ◽  
X Ray ◽  
Cell Parameters

Acetyl xylan esterase is involved in the biodegradation of hemicellulose. It cleaves O-acetyl groups from xylan, which is the most abundant hemicellulose in nature. The catalytic core of acetyl xylan esterase from T. reesei has been crystallized and X-ray diffraction data at 2.3 Å collected. The crystal belongs to the triclinic space group P1 with unit-cell parameters a = 50.3, b = 62.1, c = 40.0 Å, α = 110.1, β = 113.6 and γ = 97.9°. The asymmetric unit contains two molecules.

Refinement of the crystal structure of sieleckiite and revision of its symmetry

2017 ◽  
Vol 81 (4) ◽  
pp. 917-922
Author(s):  
Peter Elliott
Keyword(s):  
Crystal Structure ◽  
Synchrotron Radiation ◽  
Single Crystal ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Aluminium Phosphate ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Phosphate Mineral

AbstractThe crystal structure of the copper aluminium phosphate mineral sieleckiite, Cu3Al4(PO4)2 (OH)12·2H2O, from the Mt Oxide copper mine, Queensland, Australia was solved from single-crystal X-ray diffraction data utilizing synchrotron radiation. Sieleckiite has monoclinic rather than triclinic symmetry as previously reported and is space group C2/m with unit-cell parameters a = 11.711(2), b = 6.9233(14), c = 9.828(2) Å, β = 92.88(3)°, V = 795.8(3) Å3and Z = 2. The crystal structure, which has been refined to R1 = 0.0456 on the basis of 1186 unique reflections with Fo > 4σF, is a framework of corner-, edge- and face- sharing Cu and Al octahedra and PO4 tetrahedra.

Synthesis and crystal structure of (Ag,Pd)22Se6

2013 ◽  
Vol 28 (1) ◽  
pp. 13-17 ◽  
Author(s):  
F. Laufek ◽  
A. Vymazalová ◽  
D.A. Chareev ◽  
A.V. Kristavchuk ◽  
J. Drahokoupil ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Glass Tube ◽  
Structure Type ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Synthesis And Crystal Structure ◽  
X Ray ◽  
Cell Parameters ◽  
Silica Glass Tube

The (Ag,Pd)22Se6 phase was synthesized from individual elements by silica glass tube technique and structurally characterized from powder X-ray diffraction data. The (Ag,Pd)22Se6 phase crystallizes in Fm$\overline3$m symmetry, unit-cell parameters: a = 12.3169(2) Å, V = 1862.55(5) Å3, Z = 4, and Dc = 10.01 g/cm3. The crystal structure of the (Ag,Pd)22Se6 phase represents a stuffed 3a.3a.3a superstructure of the Pd structure (fcc), where only 4 from 108 available octahedral holes are occupied. Its crystal structure is related to the Cr23C6 structure type.

X-ray powder diffraction data for tetrazene nitrate monohydrate, C2H9N11O4

2021 ◽  
pp. 1-3
Author(s):  
J. Maixner ◽  
J. Ryšavý
Keyword(s):  
Cell Volume ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell Volume ◽  
Unit Cell ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

X-ray powder diffraction data, unit-cell parameters, and space group for tetrazene nitrate monohydrate, C2H9N11O4, are reported [a = 5.205(1) Å, b = 13.932(3) Å, c = 14.196(4) Å, β = 97.826(3)°, unit-cell volume V = 1019.8(4) Å3, Z = 4, and space group P21/c]. All measured lines were indexed and are consistent with the P21/c space group. No detectable impurities were observed.

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