Crystallization, molecular replacement solution, and refinement of tetrameric β-amylase from sweet potato

1995 ◽  
Vol 21 (2) ◽  
pp. 105-117 ◽  
Author(s):  
Cheom Gil Cheong ◽  
Soo Hyun Eom ◽  
Changsoo Chang ◽  
Dong Hae Shin ◽  
Hyun Kyu Song ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Molecular Replacement ◽  
Replacement Solution

Crystallization and preliminary X-ray diffraction studies of human catalase

1999 ◽  
Vol 55 (9) ◽  
pp. 1614-1615 ◽  
Author(s):  
R. A. P. Nagem ◽  
E. A. L. Martins ◽  
V. M. Gonçalves ◽  
R. Aparício ◽  
I. Polikarpov
Keyword(s):  
Search Model ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Beef Liver ◽  
X Ray ◽  
Diffusion Technique ◽  
Cell Dimensions ◽  
Synchrotron Radiation Diffraction ◽  
Replacement Solution ◽  
Unit Cell Dimensions

The enzyme catalase (H2O2–H2O2 oxidoreductase; E.C. 11.1.6) was purified from haemolysate of human placenta and crystallized using the vapour-diffusion technique. Synchrotron-radiation diffraction data have been collected to 1.76 Å resolution. The enzyme crystallized in the space group P212121, with unit-cell dimensions a = 83.6, b = 139.4, c = 227.5 Å. A molecular-replacement solution of the structure has been obtained using beef liver catalase (PDB code 4blc) as a search model.

scholarly journals Crystallization and molecular-replacement solution of a diagnostic fluorescent dye in complex with a specific Fab fragment

2007 ◽  
Vol 63 (3) ◽  
pp. 217-223 ◽  
Author(s):  
Roman C. Hillig ◽  
Siegfried Baesler ◽  
Stefanie Urlinger ◽  
Yvonne Stark ◽  
Susanne Bauer ◽  
...  
Keyword(s):  
Fluorescent Dye ◽  
Molecular Replacement ◽  
Fab Fragment ◽  
Replacement Solution

Leishmania mexicana mexicanaglucose-6-phosphate isomerase: crystallization, molecular-replacement solution and inhibition

2004 ◽  
Vol 60 (5) ◽  
pp. 915-919 ◽  
Author(s):  
Artur T. Cordeiro ◽  
Renaud Hardré ◽  
Paul A. M. Michels ◽  
Laurent Salmon ◽  
Luis F. Delboni ◽  
...  
Keyword(s):  
Molecular Replacement ◽  
Leishmania Mexicana ◽  
Replacement Solution

The molecular-replacement solution of an intermediate-sized helical polypeptide, antiamoebin I

1999 ◽  
Vol 55 (9) ◽  
pp. 1539-1545 ◽  
Author(s):  
C. F. Snook ◽  
B. A. Wallace
Keyword(s):  
Careful Consideration ◽  
Molecular Replacement ◽  
Helix Axis ◽  
Asymmetric Unit ◽  
High Resolution Data ◽  
Symmetric Structure ◽  
Structure Factors ◽  
Replacement Solution ◽  
Independent Molecules ◽  
Starting Model

The successful use of molecular-replacement methods for the solution of the intermediate-sized helical polypeptide antiamoebin I required the careful consideration of a number of parameters and exhibited some unusual characteristics when compared with molecular-replacement solutions of globular proteins. High-resolution data were required owing to several features, including the comma-like shape of the molecule (which results in a pseudo-symmetric structure at low resolution), the relative uniformity of the structure in the direction along the helix axis and the small differences between the two independent molecules in the P1 asymmetric unit. Other parameters which were important for the solution of this relatively low solvent content closely packed cell included the radius of integration, the use of normalized structure factors and especially the choice of starting model.

scholarly journals On the application of the expected log-likelihood gain to decision making in molecular replacement

2018 ◽  
Vol 74 (4) ◽  
pp. 245-255 ◽  
Author(s):  
Robert D. Oeffner ◽  
Pavel V. Afonine ◽  
Claudia Millán ◽  
Massimo Sammito ◽  
Isabel Usón ◽  
...  
Keyword(s):  
Decision Making ◽  
Measurement Errors ◽  
Single Atom ◽  
Molecular Replacement ◽  
Acta Cryst ◽  
Quickest Path ◽  
Experimental Phasing ◽  
Log Likelihood ◽  
Replacement Solution ◽  
Search Order

Molecular-replacement phasing of macromolecular crystal structures is often fast, but if a molecular-replacement solution is not immediately obtained the crystallographer must judge whether to pursue molecular replacement or to attempt experimental phasing as the quickest path to structure solution. The introduction of the expected log-likelihood gain [eLLG; McCoyet al.(2017),Proc. Natl Acad. Sci. USA,114, 3637–3641] has given the crystallographer a powerful new tool to aid in making this decision. The eLLG is the log-likelihood gain on intensity [LLGI; Read & McCoy (2016),Acta Cryst.D72, 375–387] expected from a correctly placed model. It is calculated as a sum over the reflections of a function dependent on the fraction of the scattering for which the model accounts, the estimated model coordinate error and the measurement errors in the data. It is shown how the eLLG may be used to answer the question `can I solve my structure by molecular replacement?'. However, this is only the most obvious of the applications of the eLLG. It is also discussed how the eLLG may be used to determine the search order and minimal data requirements for obtaining a molecular-replacement solution using a given model, and for decision making in fragment-based molecular replacement, single-atom molecular replacement and likelihood-guided model pruning.

Crystallization and preliminary crystallographic study of HIP/PAP, a human C-lectin overexpressed in primary liver cancers

1999 ◽  
Vol 55 (8) ◽  
pp. 1487-1489 ◽  
Author(s):  
Chantal Abergel ◽  
Sabine Chenivesse ◽  
Marie-Georges Stinnakre ◽  
Sophie Guasco ◽  
Christian Bréchot ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Adhesion Protein ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Liver Cancers ◽  
Replacement Solution

Human HIP/PAP is an adhesion protein expressed in normal pancreatic and Paneth cells and overexpressed in hepatocellular carcinoma. HIP/PAP was crystallized using the Hampton Research Crystal Screen and SAmBA software to define the optimal crystallization protocol. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 30.73, b = 49.35, c = 92.15 Å and one molecule in the asymmetric unit. Flash-frozen crystals diffract to 1.78 Å resolution using synchrotron radiation. A molecular-replacement solution was obtained using the human Reg/lithostathine structure and the AMoRe software.

Phase perturbation as a means of electron density map quality evaluation

2008 ◽  
Vol 41 (1) ◽  
pp. 31-37 ◽  
Author(s):  
Olga Kirillova
Keyword(s):  
Electron Density ◽  
Data Sets ◽  
Molecular Replacement ◽  
Data Set ◽  
Density Maps ◽  
Phase Perturbation ◽  
Replacement Solution ◽  
Electron Density Map ◽  
Trial Phase

This paper describes a new means for evaluating the quality of crystallographic electron density maps. It has been found that a better data set possesses greater robustness against perturbations applied to the phases. Thus it allows recognition of a more precise phase set and provides a way to select the best or reject the worst from several noisy data sets derived from the same crystal structure. The results indicate that calculation of the correlations by the procedure described here can be useful in ranking electron density maps in this aspect of quality. The method suggested has potential use for selecting a better molecular replacement solution, as well as for evaluating trial phase sets inab initiophasing procedures.

scholarly journals Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry

2014 ◽  
Vol 70 (2) ◽  
pp. 471-480 ◽  
Author(s):  
Joanna Sliwiak ◽  
Mariusz Jaskolski ◽  
Zbigniew Dauter ◽  
Airlie J. McCoy ◽  
Randy J. Read
Keyword(s):  
Molecular Replacement ◽  
Binding Modes ◽  
Space Group ◽  
Structure Solution ◽  
Pathogenesis Related ◽  
Replacement Solution ◽  
Symmetry Of The Solution ◽  
Multiple Copies ◽  
Statistical Effects ◽  
Insight Into

Translational noncrystallographic symmetry (tNCS) is a pathology of protein crystals in which multiple copies of a molecule or assembly are found in similar orientations. Structure solution is problematic because this breaks the assumptions used in current likelihood-based methods. To cope with such cases, new likelihood approaches have been developed and implemented inPhaserto account for the statistical effects of tNCS in molecular replacement. Using these new approaches, it was possible to solve the crystal structure of a protein exhibiting an extreme form of this pathology with seven tetrameric assemblies arrayed along thecaxis. To resolve space-group ambiguities caused by tetartohedral twinning, the structure was initially solved by placing 56 copies of the monomer in space groupP1 and using the symmetry of the solution to define the true space group,C2. The resulting structure of Hyp-1, a pathogenesis-related class 10 (PR-10) protein from the medicinal herb St John's wort, reveals the binding modes of the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS), providing insight into the function of the protein in binding or storing hydrophobic ligands.

scholarly journals Crystallization and preliminary crystallographic analysis of poly(3-hydroxybutyrate) depolymerase fromBacillus thuringiensis

2014 ◽  
Vol 70 (10) ◽  
pp. 1421-1423 ◽  
Author(s):  
Yung-Lin Wang ◽  
Yi-Ting Lin ◽  
Chia-Lin Chen ◽  
Gwo-Chyuan Shaw ◽  
Shwu-Huey Liaw
Keyword(s):  
Crystal Structure ◽  
Crystallographic Analysis ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Data Set ◽  
Cell Parameters ◽  
Replacement Solution ◽  
Potential Applications ◽  
Polymer Biodegradation ◽  
Key Enzyme

Poly[(R)-3-hydroxybutyrate] (PHB) is a microbial biopolymer that has been commercialized as biodegradable plastics. The key enzyme for the degradation is PHB depolymerase (PhaZ). A new intracellular PhaZ fromBacillus thuringiensis(BtPhaZ) has been screened for potential applications in polymer biodegradation. Recombinant BtPhaZ was crystallized using 25% polyethylene glycol 3350, 0.2 Mammonium acetate, 0.1 Mbis-tris pH 6.5 at 288 K. The crystals belonged to space groupP1, with unit-cell parametersa= 42.97,b= 83.23,c= 85.50 Å, α = 73.45, β = 82.83, γ = 83.49°. An X-ray diffraction data set was collected to 1.42 Å resolution with anRmergeof 6.4%. Unexpectedly, a molecular-replacement solution was obtained using the crystal structure ofStreptomyces lividanschloroperoxidase as a template, which shares 24% sequence identity to BtPhaZ. This is the first crystal structure of an intracellular poly(3-hydroxybutyrate) depolymerase.

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