Cluster analysis of the Biological Macromolecule Crystallization Database

Samudzi, Cleopas T.; Fivash, Matthew J.; Rosenberg, John M.

doi:10.1016/0022-0248(92)90009-8

Cited by 20 publications

(13 citation statements)

References 11 publications

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“…Initially, the Crystal Screen and Crystal Screen II kits (Hampton Research, USA) were used to screen the initial crystallizing conditions for BmK I1, BmK I4 and BmK I6; however, no crystals were found. With the solubility information provided by the screening experiments, a wide range of precipitants and pH values were tried using the grid-screen method (Samudzi & Fivash, 1992). After optimization of the conditions under which crystals appeared, good single crystals suitable for diffraction of these toxins were ®nally obtained (Fig.…”

Section: Crystallizationmentioning

confidence: 99%

Crystallization and preliminary X-ray analyses of insect neurotoxins with analgesic effect from the scorpionButhus martensiiKarsch

Guan

Liu

et al. 2000

Acta Crystallogr D Biol Cryst

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Three insect neurotoxins from the scorpion Buthus martensii Karsch, named BmK I1, BmK I4 and BmK I6, have been purified and crystallized. BmK I1 and BmK I4 show strong toxicity to insects, while BmK I6 is relatively weaker. They all exhibit an evident analgesic effect on mice; this is a novel biological function for scorpion insect toxins. Their crystals diffract to at least 3.5 (BmK I1), 2.8 (BmK I4), 2.8 (BmK I6 crystal form I) and 2.2 A (of BmK I6 crystal form II) resolution on an ordinary X-ray source. Crystals of BmK I1 belong to space group P6, with unit-cell parameters a = b = 66.2, c = 176.7 A. BmK I4 crystallized in the tetragonal space group I4, with unit-cell parameters a = b = 134.5, c = 60.6 A. BmK I6 has been crystallized in two forms: form I belongs to space group C2, with unit-cell parameters a = 46.5, b = 85.2, c = 32.6 A, beta = 110.5 degrees; form II belongs to space group R3, with the hexagonal unit-cell parameters a = b = 44.5, c = 164.7 A.

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Section: Crystallizationmentioning

confidence: 99%

Crystallization and preliminary X-ray analyses of insect neurotoxins with analgesic effect from the scorpionButhus martensiiKarsch

Guan

Liu

et al. 2000

Acta Crystallogr D Biol Cryst

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“…Nonetheless, the number of macromolecules crystallized during the past decade has increased at a near exponential rate (Gilliland & Bickham, 1990). A major contribution to this increased success has been the development of novel screening protocols and optimization strategies which have provided investigators with an expanded portfolio of effective crystallization tools (Carter & Carter, 1979;Jancarik & Kim, 1991;McPherson, 1992;Samudzi & Fivash, 1992;Stura, Nemerow & Wilson, 1992;Weber, 1990). In addition, the increasing number of investigators engaged in the crystallization of macromolecules has further enhanced the database of successful crystallization conditions and approaches.…”

Section: Introductionmentioning

confidence: 99%

“…An effective compromise to such an exhaustive search is to evaluate ranges of pH, precipitant type and precipitate concentration which have yielded high rates of success in other crystallization investigations. Based primarily upon personal experience and the contents of the NIST/CARB Biological Macromolecule Crystallization Database (BMCD), grid-screening strategies using polyethylene glycol (Mr 400 to 20 000; 6000 being the most frequently used PEG), ammonium sulfate and 2-methyl-2,4pentanediol (MPD) have proven very successful in providing initial crystallization conditions for a wide variety of proteins (Samudzi & Fivash, 1992;McPherson, 1990;Weber, 1990).…”

Section: Introductionmentioning

confidence: 99%

“…More recently, approaches for expanding the ranges of salts, polymers, organic solvents and pH included in a screen and at the same time conserving macromolecule sample, have appeared (Carter & Carter, 1979;Jancarik & Kim, 1991;McPherson, 1992;Samudzi & Fivash, 1992;Stura et al, 1992;Weber, 1990). These have seen great success in identifying initial crystallization conditions for a wide variety of macromolecules including proteins, viruses, peptides and nucleic acids.…”

Section: Introductionmentioning

confidence: 99%

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Screening and optimization strategies for macromolecular crystal growth

Cudney¹,

Patel²,

Weisgraber³

et al. 1994

Acta Cryst D

258

230

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Today the determination of successful crystallization conditions for a particular macromolecule remains a highly empirical process. Sparse-matrix and grid-screening procedures are rapid and economical means to determine preliminary crystallization conditions. During optimization the variable set (pH, precipitant type and precipitant concentration) utilized in these procedures is screened in an attempt to determine appropriate conditions for the nucleation and growth of single crystals suitable for X-ray diffraction analysis. Unfortunately, in many cases this strategy will not produce single crystals suitable for X-ray diffraction analysis. We have explored, in an empirical sense, other tools for use during optimization. First, a new screening protocol is evaluated which employs less classical precipitating agents. Second, a set of 24 electrostatic crosslinking agents are evaluated for their ability to promote crystallization. Third, a panel of more than 30 detergents are evaluated for their ability to prevent sample aggregation and influence crystal growth.

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“…Samudzi and coworkers measured the distribution of various physical parameters of the proteins crystallized and found that (1) most macromolecular molecular weights were less than 100 kDa, (2) most macromolecules crystallized at concentrations of 0.01 to 2.0 mM, and (3) the most common pH for crystallization was approximately 7.0 (Samudzi et al, 1992). The cluster analysis of the BMCD (a method that locates "natural" groupings of data within the given parameter space) showed that the data partitioned most significantly into eight groups, which showed significant asymmetry with respect to macromolecule type, crystallization method, and precipitant chemical(s) used (Samudzi et al, 1992). At the time this analysis was performed (1992), there were 1025 crystal conditions in the BMCD.…”

Section: Statistical and Empirical Analysis Of Crystallizationmentioning

confidence: 99%

The Crystallization Expert System Xtaldb, and its Application to the Structure of the 5'- nucleotidase YfbR and Other Proteins

Zimmerman

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Growing crystals is a critical step in the process of determining the 3-D structure of macromolecules by X-ray crystallography. While significant progress has been made in analyzing quantitatively crystallization experiments, in general, crystallization of biological macromolecules remains more of an art than a science. This work presents Xtaldb, an expert system for the quantitative analysis of crystallization experiments.Xtaldb provides tools for efficiently designing crystallization screens, tracks in a semiautomatic manner most of the parameters of the experiments, and provides sophisticated search, analysis, and data graphing tools. The algorithm used to produce balanced random screens is the fastest and most robust available. Xtaldb was tested on a set of six novel proteins that had failed to produce diffraction-quality crystals in a high-throughput structure determination pipeline. Of them, five yielded crystals diffracting to 3.5 Å or better and three 3-D structures were elucidated. One of the three proteins was YfbR, a member of the HD-domain phosphohydrolase superfamily. Structural analysis of the 3-D structure and biochemical work confirmed phosphohydrolase activity. Further studies by a collaborator demonstrated that YfbR is a 5'-deoxynucleotidase. Xtaldb was used to produce two crystals of catalytically inactive YfbR mutants in the presence of metal cofactor and the substrates TMP or dAMP. The structures of the complexes explained the mechanism of the unique pattern of substrate selectivity, further supported by computational docking studies. The complex structures suggested a plausible atomic mechanism of catalysis for the enzyme, the first proposed mechanism for an HD-domain phosphohydrolase based directly from enzyme-substrate complex structures.

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Cluster analysis of the Biological Macromolecule Crystallization Database

Cited by 20 publications

References 11 publications

Crystallization and preliminary X-ray analyses of insect neurotoxins with analgesic effect from the scorpionButhus martensiiKarsch

Crystallization and preliminary X-ray analyses of insect neurotoxins with analgesic effect from the scorpionButhus martensiiKarsch

Screening and optimization strategies for macromolecular crystal growth

The Crystallization Expert System Xtaldb, and its Application to the Structure of the 5'- nucleotidase YfbR and Other Proteins

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Cluster analysis of the Biological Macromolecule Crystallization Database

Cited by 20 publications

References 11 publications

Crystallization and preliminary X-ray analyses of insect neurotoxins with analgesic effect from the scorpionButhus martensiiKarsch

Crystallization and preliminary X-ray analyses of insect neurotoxins with analgesic effect from the scorpionButhus martensiiKarsch

Screening and optimization strategies for macromolecular crystal growth

The Crystallization Expert System Xtaldb, and its Application to the Structure of the 5&#39;- nucleotidase YfbR and Other Proteins

Contact Info

Product

Resources

About

The Crystallization Expert System Xtaldb, and its Application to the Structure of the 5'- nucleotidase YfbR and Other Proteins