Structure of Monellin Refined to 2.3 Å Resolution in the Orthorhombic Crystal Form

1997 ◽  
Vol 53 (6) ◽  
pp. 713-719 ◽  
Author(s):  
G. Bujacz ◽  
M. Miller ◽  
R. Harrison ◽  
N. Thanki ◽  
G. L. Gilliland ◽  
...  
Keyword(s):  
Crystal Form ◽  
Orthorhombic Crystal

scholarly journals Two polymorphs of 1,8-dichloroanthracene

2013 ◽  
Vol 69 (2) ◽  
pp. 199-203 ◽  
Author(s):  
Peter Müller ◽  
Frank R. Fronczek ◽  
Stacey J. Smith ◽  
Teresa Mako ◽  
Mindy Levine
Keyword(s):  
Low Temperature ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Crystal Form ◽  
Temperature Structure ◽  
Orthorhombic Crystal ◽  
Acta Cryst ◽  
Monoclinic Form ◽  
Compound C ◽  
Dimensional Network

A second, monoclinic, polymorph of the title compound, C14H8Cl2, has been found. In addition to the structure of this monoclinic form, the structure of the previously described orthorhombic form [Desvergne, Chekpo & Bouas-Laurent (1978).J. Chem. Soc. Perkin Trans. 2, pp. 84–87; Benites, Maverick & Fronczek (1996).Acta Cryst.C52, 647–648] has been redetermined at low temperature and using modern methods. The low-temperature structure of the orthorhombic form is of significantly higher quality than the previously published structure and additional details can be derived. A comparison of the crystal packing of the two forms with a focus on weak intermolecular C—H...Cl interactions shows the monoclinic structure to have one such interaction linking the molecules into infinite ribbons, while two crystallographically independent C—H...Cl interactions give rise to an interesting infinite three-dimensional network in the orthorhombic crystal form.

Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase

2014 ◽  
Vol 70 (12) ◽  
pp. 3099-3109 ◽  
Author(s):  
Dmitry Zamyatkin ◽  
Chandni Rao ◽  
Elesha Hoffarth ◽  
Gabriela Jurca ◽  
Hayeong Rho ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Covalent Bond ◽  
Crystal Form ◽  
Phosphoryl Group ◽  
Nucleoside Triphosphate ◽  
Orthorhombic Crystal ◽  
Crystal Forms ◽  
Terminal Nucleotide ◽  
Thumb Domain

The RNA-dependent RNA polymerase (RdRP) from norovirus (NV) genogroup II has previously been crystallized as an apoenzyme (APO1) in multiple crystal forms, as well as as a pre-incorporation ternary complex (PRE1) bound to Mn2+, various nucleoside triphosphates and an RNA primer-template duplex in an orthorhombic crystal form. When crystallized under near-identical conditions with a slightly different RNA primer/template duplex, however, the enzyme–RNA complex forms tetragonal crystals (anisotropic data,dmin≃ 1.9 Å) containing a complex with the primer/template bound in a backtracked state (BACK1) similar to a post-incorporation complex (POST1) in a step of the enzymatic cycle immediately following nucleotidyl transfer. The BACK1 conformation shows that the terminal nucleotide of the primer binds in a manner similar to the nucleoside triphosphate seen in the PRE1 complex, even though the terminal two phosphoryl groups in the triphosphate moiety are absent and a covalent bond is present between the α-phosphoryl group of the terminal nucleotide and the 3′-oxygen of the penultimate nucleotide residue. The two manganese ions bound at the active site coordinate to conserved Asp residues and the bridging phosphoryl group of the terminal nucleotide. Surprisingly, the conformation of the thumb domain in BACK1 resembles the open APO1 state more than the closed conformation seen in PRE1. The BACK1 complex thus reveals a hybrid state in which the active site is closed while the thumb domain is open. Comparison of the APO1, PRE1 and BACK1 structures of NV polymerase helps to reveal a more complete and complex pathway of conformational changes within a single RdRP enzyme system. These conformational changes lend insight into the mechanism of RNA translocation following nucleotidyl transfer and suggest novel approaches for the development of antiviral inhibitors.

An orthorhombic crystal form of cyclohexaicosaose, CA26·32.59 H2O: comparison with the triclinic form

2001 ◽  
Vol 336 (2) ◽  
pp. 141-153 ◽  
Author(s):  
Olaf Nimz ◽  
Katrin Geßler ◽  
Isabel Usón ◽  
Wolfram Saenger
Keyword(s):  
Crystal Form ◽  
Orthorhombic Crystal ◽  
Triclinic Form

Structure of an insulin dimer in an orthorhombic crystal: the structure analysis of a human insulin mutant (B9 Ser→Glu)

1999 ◽  
Vol 55 (9) ◽  
pp. 1524-1532 ◽  
Author(s):  
Zhi-Ping Yao ◽  
Zong-Hao Zeng ◽  
Hong-Min Li ◽  
Ying Zhang ◽  
You-Min Feng ◽  
...  
Keyword(s):  
Human Insulin ◽  
Solution Structure ◽  
Building Blocks ◽  
Structural Rearrangement ◽  
Crystal Form ◽  
Terminal Segment ◽  
Orthorhombic Crystal ◽  
Amino Terminal ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The structure of human insulin mutant B9 (Ser→Glu) was determined by an X-ray crystallographic method at 2.5 Å resolution with an R factor of 0.165 under non-crystallographic restraints. The crystals were grown at low pH (<3.8) and belong to the orthorhombic P212121 space group with unit-cell dimensions a = 44.54, b = 46.40, c = 51.85 Å and one dimer per asymmetric unit without further aggregation. The structure in this crystal form can be regarded as a model for a discrete insulin dimer and displays the following features compared with the structure of 2Zn insulin. (i) The overall dimer is expanded and more symmetric. The two A chains are about 2 Å more distant from each other, while the two B chains are about 0.8 Å further apart. Both monomers are more similar to molecule 1 than molecule 2 of the 2Zn insulin dimer. (ii) The dimer structure is stabilized by protonation and neutralization of the carboxyl groups at lower pH and, in addition, by formation of a hydrogen-bond network among the side chains of residues GluB9, HisB13 and HisB10 on the dimer-forming surface of both monomers, resulting from a structural rearrangement. (iii) The B-chain amino-terminal segment is in an open state (O state), i.e. a state different from the well known R and T states found in the insulin hexamer. In the O state, the B-chain N-terminal segment is in an extended conformation and is detached from the rest of the molecule. This conformational state has also been observed in the monomeric crystal structure of despentapeptide (B26–B30) and desheptapeptide (B24–B30) insulin, as well as in the solution structure of an engineered insulin monomer. It suggests that the O state may be the characteristic conformation of insulin in lower aggregation forms and may be relevant to the formation of insulin fibrils. In addition, based on the crystallization process, the smallest possible building blocks of insulin crystal are also discussed.

scholarly journals High-density polyethylene crystals with double melting peaks induced by ultra-high-molecular-weight polyethylene fibre

2018 ◽  
Vol 5 (7) ◽  
pp. 180394 ◽  
Author(s):  
Weijun Miao ◽  
Hao Zhu ◽  
Tianchen Duan ◽  
Hongbing Chen ◽  
Feng Wu ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
High Density Polyethylene ◽  
Fibre Composite ◽  
Crystal Form ◽  
High Density ◽  
Scanning Calorimetry ◽  
Orthorhombic Crystal ◽  
Fibre Composites ◽  
Ultra High Molecular Weight

High-density polyethylene (HDPE)/ultra-high-molecular-weight polyethylene (UHMWPE) fibre composites were prepared via solution crystallization to investigate the components of epitaxial crystal growth on a highly oriented substrate. Scanning electron microscopy morphologies of HDPE crystals on UHMWPE fibres revealed that the edge-on ribbon pattern crystals that were formed initially on UHMWPE fibres converted afterwards to a sheet shape as crystallization progressed. Wide-angle X-ray diffraction confirmed that the polymer chain oriented along the fibre axis and the orthorhombic crystal form of HDPE remained unchanged in HDPE/UHMWPE fibre composite systems. The thermal behaviour of the fibre composites measured by differential scanning calorimetry showed double melting peaks, the nature of which, as disclosed by partial melting experiments, is ascribed to bilayer components existing in the induced crystals: the inner layer is composed of more regularly folded chain crystals induced by UHMWPE fibres, and the outer layer formed on the inner one with a thinner and lower ordered crystal structure.

X-ray Structure of the ZnII β-Lactamase from Bacteroides fragilis in an Orthorhombic Crystal Form

1998 ◽  
Vol 54 (1) ◽  
pp. 47-57 ◽  
Author(s):  
Andrea Carfi ◽  
Emile Duée ◽  
Raquel Paul-Soto ◽  
Moreno Galleni ◽  
Jean-Marie Frère ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Bacteroides Fragilis ◽  
Crystal Form ◽  
Water Molecules ◽  
Orthorhombic Crystal ◽  
X Ray ◽  
Class B ◽  
Catalytic Mechanisms ◽  
Zn Ions

β-Lactamases are extracellular or periplasmic bacterial enzymes which confer resistance to β-lactam antibiotics. On the basis of their catalytic mechanisms, they can be divided into two major groups: active-site serine enzymes (classes A, C and D) and the ZnII enzymes (class B). The first crystal structure of a class B enzyme, the metallo-β-lactamase from Bacillus cereus, has been solved at 2.5 Å resolution [Carfi, Pares, Duée, Galleni, Duez, Frère & Dideberg (1995). EMBO J. 14, 4914–4921]. Recently, the crystal structure of the metallo-β-lactamase from Bacteroides fragilis has been determined in a tetragonal space group [Concha, Rasmussen, Bush & Herzberg (1996). Structure, 4, 823–836]. The structure of the metallo-β-lactamase from B. fragilis in an orthorhombic crystal form at 2.0 Å resolution is reported here. The final crystallographic R is 0.196 for all the 32 501 observed reflections in the range 10–2.0 Å. The refined model includes 458 residues, 437 water molecules, four zinc and two sodium ions. These structures are discussed with reference to Zn binding and activity. A catalytic mechanism is proposed which is coherent with metallo-β-lactamases being active with either one Zn ion (as in Aeromonas hydrophila) or two Zn ions (as in B. fragilis) bound to the protein.

The structures of α2u-globulin and its complex with a hyaline droplet inducer

1999 ◽  
Vol 55 (4) ◽  
pp. 753-762 ◽  
Author(s):  
Barnali N. Chaudhuri ◽  
Gerard J. Kleywegt ◽  
Joakim Björkman ◽  
Lois D. Lehman-McKeeman ◽  
Joel D. Oliver ◽  
...  
Keyword(s):  
Crystal Form ◽  
Urinary Protein ◽  
Male Rats ◽  
Male Rat ◽  
Diverse Group ◽  
Orthorhombic Crystal ◽  
Major Urinary Protein ◽  
Monoclinic Crystal ◽  
Renal Carcinogenesis ◽  
Rate Determining Step

α2u-Globulin (A2U) is the major urinary protein excreted by adult male rats. The structure of a monoclinic crystal form of A2U was reported in 1992 [Böcskei et al. (1992). Nature (London), 360, 186–188]. The structures of an orthorhombic crystal form of A2U at 2.5 Å resolution (refined to an R factor of 0.248; R free = 0.264) and of a complex between A2U and d-limonene 1,2-epoxide (DLO) at 2.9 Å resolution (R factor = 0.248; R free = 0.260) are presented here. DLO is one of a diverse group of chemicals which cause a male rat-specific renal carcinogenesis called hyaline-droplet nephropathy. The rate-determining step in the development of this disorder is the binding of the toxin to A2U. Comparison of the cavities in A2U and in the corresponding mouse urinary protein (MUP) reveal that the former is tailor-made for small oval hydrophobic ligands such as DLO. The cavity in MUP is more shallow and elongated and cannot easily accommodate such ligands.

scholarly journals Controlled dehydration, structural flexibility and gadolinium MRI contrast compound binding in the human plasma glycoprotein afamin

2019 ◽  
Vol 75 (12) ◽  
pp. 1071-1083 ◽  
Author(s):  
Andreas Naschberger ◽  
Pauline Juyoux ◽  
Jill von Velsen ◽  
Bernhard Rupp ◽  
Matthew W. Bowler
Keyword(s):  
Computational Modelling ◽  
Crystal Form ◽  
Human Albumin ◽  
Conformational State ◽  
Crystallographic Structure ◽  
Human Blood Plasma ◽  
Orthorhombic Crystal ◽  
Monoclinic Form ◽  
Plasma Glycoprotein ◽  
Multiple Challenges

Afamin, which is a human blood plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome, poses multiple challenges for crystallographic structure determination, both practically and in analysis of the models. Several hundred crystals were analysed, and an unusual variability in cell volume and difficulty in solving the structure despite an ∼34% sequence identity with nonglycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite the simplified glycosylation in insect cell-expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilize the orthorhombic crystal form, reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational state of the protein. An iterative strategy using fully automatic experiments available on MASSIF-1 was used to quickly determine the optimal protocol to achieve the phase transition, which should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computational modelling purposes given that the conformational state of the binding sites and the electron density in the binding site, which is likely to result from PEGs, greatly varies between models. This also holds for the analysis of nonspecific low-affinity ligands, where often a variety of fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin also seems to bind gadoteridol, a magnetic resonance imaging contrast compound, in at least two sites. One pair of gadoteridol molecules is located near the human albumin Sudlow site, and a second gadoteridol molecule is located at an intermolecular site in proximity to domain IA. The data from the co-crystals support modern metrics of data quality in the context of the information that can be gleaned from data sets that would be abandoned on classical measures.

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