From crystal to structure in 84 years

What is it?

In 1926 Jack Bean urease was the first protein to be crystallised 1, earning a place in the history books for this humble plant protein and a Nobel Prize for James B. Sumner (see yesterday’s post for more). Besides establishing that proteins could be crystallised, Sumner’s work was remarkable for demonstrating that proteins could be isolated and purified whilst retaining enzymatic activity. Despite this landmark advance in protein biochemistry and crystallography, it was a further 84 years before the crystal structure of Jack Bean Urease was determined, in what must surely be the longest running crystallography endeavour in history2.

Where did the structure come from?

Urease is an enzyme in plants, bacteria and fungi that helps to break urea into ammonia and carbon dioxide. Whilst other urease structures were known – for example Helicobacter pylori urease, the structure of which helped to explain how this bacterium can survive in the acid environment of the human stomach3 – the structure of Jack Bean urease was only determined in 2010.

What does it look like?

Urease

Plant ureases are single chain proteins. Jack Bean urease is a T-shaped molecule of four domains (coloured here in red, blue, yellow and pink.) In common with other ureases, Jack Bean Ureases binds two nickel ions (blue spheres) in its active site; these are required for enzymatic breakdown of urea.

This structure is Protein Data Bank ID 3LA4

References

  1. Sumner, 1926: J. Biol. Chem. 69:435-441
  2. Balasubramanian & Ponnuraj. 2010 J. Mol. Biol. 400:274-283
  3. Ha et al., 2001. Nature Structural Biology 8: 505-509
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Five fold – Cobalt tricyanomethanide

What is it?

five_fold

The beautiful shapes of crystals are not a fluke – they reflect the symmetries of the atoms within the crystal. Those atoms (and molecules), however, can only have certain types of symmetries. Five-fold symmetry, for example, is not possible (except for quasicrystals, which are a whole different story…). You can prove this to yourself – try covering the whole surface of a table only with regular pentagons. Can’t do it can you? There are always those annoying gaps. So when the beautiful pentagonal “crystals” shown above were discovered in a reaction, there had to be more going on. For a crystallographer five fold symmetry sets off alarm bells.

It turns out that these crystals weren’t individual crystals at all, but rather collections of five individual wedge-shaped crystals growing together to form a pentagon. The structure of the crystals was solved by carefully cutting out one of these wedges and performing X-ray diffraction on this. If the pentagon had of been used instead it would have been a horrible, unsolvable mess, with five diffraction patterns superimposed on each other, all in different orientations.

Solving the crystal structure revealed not only the molecular structure of the crystals, but also solved another curious observation. While the compound made with cobalt formed the lovely orange pentagons you see here, similar compounds with other metals formed pentagons with wedges missing. Even more unusually, crystals of the copper analogue didn’t form the pentagons at all.

The key to solving this riddle was the fact that the lovely sharp arrangement of faces on a crystal are related to the arrangements of simple planes of atoms within the crystal (as I said before, the shapes of crystals are related to the symmetry of the atoms within). In the structures in question, there are two very simple planes in the crystals that are angled at approximately 72 °, which is exactly the right angle you need for the corner of the wedges that come together in the middle of the pentagon. For the cobalt structure, that angle was 71.2°, and only pentagons formed. For the other structures, results and angles varied. Mn (71.7°) and Cd (72.2°) were closer to the magic 72°, but maybe too close for comfort. These only formed pentagons with wedges missing, or wedges by themselves. Zn, with an angle further way (70.9°) was similar. Ni (70.8°) formed pentagons, but they were very small and too a lot of effort to make. Cu, with the greatest deviation from 72 ° (67.3°), formed no pentagons at all.

What does it look like?

five_fold_2

So after all that, what was the structure? It turned out that the structure was very closely related to that of the mineral rutile. In these new structures, however, the titanium atoms in rutile were replaced by the transition metals listed above, and the oxygen atoms were replaced by the larger tricyanomethanide anion. Because the anion was much larger in new structures, there was room enough in the structure for not one but two networks to coexist, weaving through each other (but never touching) in an intricate dance known as interpenetration. It pays to look at your crystals closely. Their shape can tell you something if you’re taking notice.

 

Where did the structure come from?

“Crystal structures and magnetic properties of the interpenetrating rutile-related compounds M(tcm)2 [M = octahedral, divalent metal; tcm- = tricyanomethanide, C(CN)3] and the sheet structures of [M(tcm)2(EtOH)2] (M = Co or Ni)”, S.R. Batten, B.F. Hoskins, B. Moubaraki, K.S. Murray and R. Robson, J. Chem. Soc., Dalton Trans., 1999, 2977.

CCDC Refcode: LORGAA

Selenite – Crystal Cathedrals

What is it?

It is the dream of all crystallographers to develop a technique which can grow the largest and highest quality crystals possible. Often this is extremely difficult to do due to all of the competing factors which can drive crystal growth, and so it is often considered an art form. The rarity of large single crystals is what makes the Naica crystal caves truly extraordinary.

The great crystal cavern of NAICA mines.

The great crystal cavern of NAICA mines.

Buried 300 meters below the surface, and discovered at a time when we people believed that they had seen every spectacular sight the earth had to offer, are the selenite crystal caves (Figure 1). No, this is not a carefully constructed Photoshop; those are real people climbing over pure gypsum crystals, otherwise known as selenite. In fact these are the largest of any naturally occurring crystals measuring up to 12 m in length, 4 m in diameter and 55 tons in weight. However, before you rush to pull out your passport and start booking flights, know that these caves are not open to the public. The caves are restricted partially for preservation purposes (instigated by a mining company of all things) but also because conditions within the cave are oppressive. Due to their location above an underground magma chamber and the presence of a large quantity of ground water, temperatures can sit at a constant 58 °C and 90 to 99 % humidity. Without special protection humans can only survive in these conditions for a few minutes. Incidentally, these are ideal conditions for crystal growth. Prior to their discovery, the caves were filled with hot, mineral rich water for 500,000 years. During this time the temperature hardly varied and the crystals were allowed to slowly grow to the size they are today.[1]

Researcher in protective gear among the crystals.

Researcher in protective gear among the crystals.

So if the caves are closed to public access, what are people doing there? A huge research project is being undertaken covering fields from medical research to regional geology. Some examples of the research being performed include, investigating how the crystals became so large and how old they are, studying pollen and microorganisms trapped inside the crystals, developing technology which enables humans to work in extreme conditions for long periods of time and building an understanding of the physiological effects of exposure to these extreme conditions over a long period of time. However, the longer the crystals are exposed to the air the more faded and brittle they become, eventually cracking under their own weight. As a result there are constant discussions on whether research should continue in order to understand this unique natural resource or whether the caves should be re-flooded with water in order to preserve their current form.

What does it look like?

Structure was generated in VESTA

Structure was generated in VESTA

As mentioned, the crystals are a pure form of gypsum known as selenite. The crystal structure of selenite/gypsum (CaSO4•2(H2O)) has been featured before on this blog in its “desert rose form”. The main difference between the desert rose crystals and selenite is the presence of sand impurities in desert rose. Another view of the structure is provided below where calcium is shown in blue, SO4 tetrahedra are yellow, oxygen is red and hydrogen is white.

Where did the structure come from?

The image was generated from a structure in the paper Schofield P. F., Knight K. S., Stretton I. C. American Mineralogist 81 (1996) 847-851 and can be found on the American Mineralogical database.

Images from:

Cave of Crystal Giants – National Geographic Magazine, Available from: <http://ngm.nationalgeographic.com/2008/11/crystal-giants/shea-text&gt; [November 2008]

[1]          NAICA PROJECT/CRYSTALS’ CAVE, Available from: <http://www.naica.com.mx/english/internas/interna4_1.htm&gt; [Accessed May 2014]