2lzm
From Proteopedia
(New page: 200px<br /><applet load="2lzm" size="450" color="white" frame="true" align="right" spinBox="true" caption="2lzm, resolution 1.7Å" /> '''STRUCTURE OF BACTERIO...) |
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| - | [[Image:2lzm.jpg|left|200px]]<br /><applet load="2lzm" size=" | + | [[Image:2lzm.jpg|left|200px]]<br /><applet load="2lzm" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2lzm, resolution 1.7Å" /> | caption="2lzm, resolution 1.7Å" /> | ||
'''STRUCTURE OF BACTERIOPHAGE T4 LYSOZYME REFINED AT 1.7 ANGSTROMS RESOLUTION'''<br /> | '''STRUCTURE OF BACTERIOPHAGE T4 LYSOZYME REFINED AT 1.7 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of the lysozyme from bacteriophage T4 has been refined at | + | The structure of the lysozyme from bacteriophage T4 has been refined at 1.7 A resolution to a crystallographic residual of 19.3%. The final model has bond lengths and bond angles that differ from "ideal" values by 0.019 A and 2.7 degrees, respectively. The crystals are grown from electron-dense phosphate solutions and the use of an appropriate solvent continuum substantially improved the agreement between the observed and calculated structure factors at low resolution. Apart from changes in the conformations of some side-chains, the refinement confirms the structure of the molecule as initially derived from a 2.4 A resolution electron density map. There are 118 well-ordered solvent molecules that are associated with the T4 lysozyme molecule in the crystal. Four of these are more-or-less buried. There is a clustering of water molecules within the active site cleft but, other than this, the solvent molecules are dispersed around the surface of the molecule and do not aggregate into ice-like structures or pentagonal or hexagonal clusters. The apparent motion of T4 lysozyme in the crystal can be interpreted in terms of significant interdomain motion corresponding to an opening and closing of the active site cleft. For the amino-terminal domain the motion can be described equally well (correlation coefficients approx. 0.87) as quasi-rigid-body motion either about a point or about an axis of rotation. The motion in the crystals of the carboxy-terminal domain is best described as rotation about an axis (correlation coefficient 0.80) although in this case the apparent motion seems to be influenced in part by crystal contacts and may be of questionable relevance to dynamics in solution. |
==About this Structure== | ==About this Structure== | ||
| - | 2LZM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. This structure | + | 2LZM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. This structure supersedes the now removed PDB entry 1LZM. 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=2LZM OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Lysozyme]] | [[Category: Lysozyme]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Matthews, B | + | [[Category: Matthews, B W.]] |
| - | [[Category: Weaver, L | + | [[Category: Weaver, L H.]] |
[[Category: hydrolase (o-glycosyl)]] | [[Category: hydrolase (o-glycosyl)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:07:19 2008'' |
Revision as of 16:07, 21 February 2008
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STRUCTURE OF BACTERIOPHAGE T4 LYSOZYME REFINED AT 1.7 ANGSTROMS RESOLUTION
Overview
The structure of the lysozyme from bacteriophage T4 has been refined at 1.7 A resolution to a crystallographic residual of 19.3%. The final model has bond lengths and bond angles that differ from "ideal" values by 0.019 A and 2.7 degrees, respectively. The crystals are grown from electron-dense phosphate solutions and the use of an appropriate solvent continuum substantially improved the agreement between the observed and calculated structure factors at low resolution. Apart from changes in the conformations of some side-chains, the refinement confirms the structure of the molecule as initially derived from a 2.4 A resolution electron density map. There are 118 well-ordered solvent molecules that are associated with the T4 lysozyme molecule in the crystal. Four of these are more-or-less buried. There is a clustering of water molecules within the active site cleft but, other than this, the solvent molecules are dispersed around the surface of the molecule and do not aggregate into ice-like structures or pentagonal or hexagonal clusters. The apparent motion of T4 lysozyme in the crystal can be interpreted in terms of significant interdomain motion corresponding to an opening and closing of the active site cleft. For the amino-terminal domain the motion can be described equally well (correlation coefficients approx. 0.87) as quasi-rigid-body motion either about a point or about an axis of rotation. The motion in the crystals of the carboxy-terminal domain is best described as rotation about an axis (correlation coefficient 0.80) although in this case the apparent motion seems to be influenced in part by crystal contacts and may be of questionable relevance to dynamics in solution.
About this Structure
2LZM is a Single protein structure of sequence from Bacteriophage t4. This structure supersedes the now removed PDB entry 1LZM. Active as Lysozyme, with EC number 3.2.1.17 Full crystallographic information is available from OCA.
Reference
Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution., Weaver LH, Matthews BW, J Mol Biol. 1987 Jan 5;193(1):189-99. PMID:3586019
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