1lma: Difference between revisions

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PROTEIN HYDRATION AND WATER STRUCTURE: X-RAY ANALYSIS OF A CLOSELY PACKED PROTEIN CRYSTAL WITH VERY LOW SOLVENT CONTENT

OverviewOverview

Low-humidity monoclinic lysozyme, resulting from a water-mediated transformation, has one of the lowest solvent contents (22% by volume) observed in a protein crystal. Its structure has been solved by the molecular replacement method and refined to an R value of 0.175 for 7684 observed reflections in the 10-1.75 A resolution shell. 90% of the solvent in the well ordered crystals could be located. Favourable sites of hydration on the protein surface include side chains with multiple hydrogen-bonding centres, and regions between short hydrophilic side chains and the main-chain CO or NH groups of the same or nearby residues. Major secondary structural features are not disrupted by hydration. However, the free CO groups at the C terminii and, to a lesser extent, the NH groups at the N terminii of helices provide favourable sites for water interactions, as do reverse turns and regions which connect beta-structure and helices. The hydration shell consists of discontinuous networks of water molecules, the maximum number of molecules in a network being ten. The substrate-binding cleft is heavily hydrated, as is the main loop region which is stabilized by water interactions. The protein molecules are close packed in the crystals with a molecular coordination number of 14. Arginyl residues are extensively involved in intermolecular hydrogen bonds and water bridges. The water molecules in the crystal are organized into discrete clusters. A distinctive feature of the clusters is the frequent occurrence of three-membered rings. The protein molecules undergo substantial rearrangement during the transformation from the native to the low-humidity form. The main-chain conformations in the two forms are nearly the same, but differences exist in the side-chain conformation. The differences are particularly pronounced in relation to Trp 62 and Trp 63. The shift in Trp 62 is especially interesting as it is also known to move during inhibitor binding.

About this StructureAbout this Structure

1LMA is a Single protein structure of sequence from Gallus gallus with as ligand. Active as Lysozyme, with EC number 3.2.1.17 Full crystallographic information is available from OCA.

ReferenceReference

Protein hydration and water structure: X-ray analysis of a closely packed protein crystal with very low solvent content., Madhusudan, Kodandapani R, Vijayan M, Acta Crystallogr D Biol Crystallogr. 1993 Mar 1;49(Pt 2):234-45. PMID:15299529

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-[[Image:1lma.gif|left|200px]]<br /><applet load="1lma" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1lma, resolution 1.75&Aring;" />
 '''PROTEIN HYDRATION AND WATER STRUCTURE: X-RAY ANALYSIS OF A CLOSELY PACKED PROTEIN CRYSTAL WITH VERY LOW SOLVENT CONTENT'''<br />
 ==Overview==
-Low-humidity monoclinic lysozyme, resulting from a water-mediated, transformation, has one of the lowest solvent contents (22% by volume), observed in a protein crystal. Its structure has been solved by the, molecular replacement method and refined to an R value of 0.175 for 7684, observed reflections in the 10-1.75 A resolution shell. 90% of the solvent, in the well ordered crystals could be located. Favourable sites of, hydration on the protein surface include side chains with multiple, hydrogen-bonding centres, and regions between short hydrophilic side, chains and the main-chain CO or NH groups of the same or nearby residues., Major secondary structural features are not disrupted by hydration., However, the free CO groups at the C terminii and, to a lesser extent, the, NH groups at the N terminii of helices provide favourable sites for water, interactions, as do reverse turns and regions which connect beta-structure, and helices. The hydration shell consists of discontinuous networks of, water molecules, the maximum number of molecules in a network being ten., The substrate-binding cleft is heavily hydrated, as is the main loop, region which is stabilized by water interactions. The protein molecules, are close packed in the crystals with a molecular coordination number of, 14. Arginyl residues are extensively involved in intermolecular hydrogen, bonds and water bridges. The water molecules in the crystal are organized, into discrete clusters. A distinctive feature of the clusters is the, frequent occurrence of three-membered rings. The protein molecules undergo, substantial rearrangement during the transformation from the native to the, low-humidity form. The main-chain conformations in the two forms are, nearly the same, but differences exist in the side-chain conformation. The, differences are particularly pronounced in relation to Trp 62 and Trp 63., The shift in Trp 62 is especially interesting as it is also known to move, during inhibitor binding.
+Low-humidity monoclinic lysozyme, resulting from a water-mediated transformation, has one of the lowest solvent contents (22% by volume) observed in a protein crystal. Its structure has been solved by the molecular replacement method and refined to an R value of 0.175 for 7684 observed reflections in the 10-1.75 A resolution shell. 90% of the solvent in the well ordered crystals could be located. Favourable sites of hydration on the protein surface include side chains with multiple hydrogen-bonding centres, and regions between short hydrophilic side chains and the main-chain CO or NH groups of the same or nearby residues. Major secondary structural features are not disrupted by hydration. However, the free CO groups at the C terminii and, to a lesser extent, the NH groups at the N terminii of helices provide favourable sites for water interactions, as do reverse turns and regions which connect beta-structure and helices. The hydration shell consists of discontinuous networks of water molecules, the maximum number of molecules in a network being ten. The substrate-binding cleft is heavily hydrated, as is the main loop region which is stabilized by water interactions. The protein molecules are close packed in the crystals with a molecular coordination number of 14. Arginyl residues are extensively involved in intermolecular hydrogen bonds and water bridges. The water molecules in the crystal are organized into discrete clusters. A distinctive feature of the clusters is the frequent occurrence of three-membered rings. The protein molecules undergo substantial rearrangement during the transformation from the native to the low-humidity form. The main-chain conformations in the two forms are nearly the same, but differences exist in the side-chain conformation. The differences are particularly pronounced in relation to Trp 62 and Trp 63. The shift in Trp 62 is especially interesting as it is also known to move during inhibitor binding.
 ==About this Structure==
-LMA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with NO3 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LMA OCA].
+LMA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with <scene name='pdbligand=NO3:'>NO3</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LMA OCA].
 ==Reference==
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 [[Category: hydrolase(o-glycosyl)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:40:27 2007''
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