User Stories:ROP four-helix bundle - Revision history

WikiSysop: add image

2009-07-16T14:16:55Z

add image

WikiSysop: correct script

2009-07-11T21:56:25Z

correct script

WikiSysop: reformat as per template

2009-07-11T21:54:01Z

reformat as per template

Airlie: Initialize from paper

2009-07-09T09:57:29Z

Initialize from paper

New page

The A31P mutant of ROP forms a helix–turn–helix motif that homodimerizes to form a four-helix bundle. The asymmetric unit contains two copies of the helix–turn–helix motif (Glykos & Kokkinidis, 2003; Fig. 4b). The structure was originally solved with a 26-residue polyalanine single helix as the model and an extremely computationally intensive 23- dimensional Monte-Carlo search implemented in the program Queen of Spades (Glykos & Kokkinidis, 2001). The command script for the solution of the ROP four-helix
bundle using the ‘automated MR’ mode of Phaser is shown in Appendix A2. The r.m.s. deviation for ROP is given as 1.0 Å ,since the sequence identity of the polyalanine helix is not a valid estimation of the r.m.s. deviation between the polyalanine helix and the backbone atoms of the ROP structure. The r.m.s. deviation value of 1.0 Å is a reasonable guess. Phaser produces eight solutions after a tree search with hundreds of branches, especially in the search for the second of the four helices. The eight solutions are nearly identical, differing only in the registration of the model to the structure helices (i.e. the Cα residues slip up or down the helix). All eight solutions generate a complete structure after model building with ARP/wARP (Perrakis et al., 2001). Although many potential solutions are stored in the intermediate stages of the search, the search itself is not computationally intensive.

← Older revision		Revision as of 14:16, 16 July 2009
Line 50:		Line 50:
	:McCoy AJ		:McCoy AJ
	:Acta Cryst. (2007). D63, 32-41		:Acta Cryst. (2007). D63, 32-41
		+
		+	;Figures
		+	[[Image:ROP.gif\|left\|frame\|Structure of the ROP four-helix bundle structure. The asymmetric unit is
		+	shown in red and crystallographically related molecules are shown in white. Together, they form two
		+	four-helix bundles.]]

@@ Line 39: / Line 39: @@
 <pre>
 MODE MR_AUTO
-HKLIN beta_blip.mtz
+HKLIN A31P.mtz
-LABIN F=Fobs SIGF=Sigma
+LABIN F=FP SIGF=SIGFP
-ENSEMBLE BETA PDB beta.pdb ID 100
+COMPOSITION PROTEIN MW 6106 NUM 2
-ENSEMBLE BLIP PDB blip.pdb ID 100
+ENSEMBLE helix PDB helix.pdb RMS 1.0
-SEARCH ENSEMBLE BETA
+SEARCH ENSEMBLE helix NUM 4
 </pre>

← Older revision		Revision as of 21:54, 11 July 2009
Line 1:		Line 1:
−	The A31P mutant of ROP forms a helix–turn–helix motif that homodimerizes to form a four-helix bundle. The asymmetric unit contains two copies of the helix–turn–helix motif ~~(Glykos & Kokkinidis, 2003; Fig. 4b)~~. The structure was originally solved with a 26-residue polyalanine single helix as the model and an extremely computationally intensive 23- dimensional Monte-Carlo search implemented in the program Queen of Spades ~~(Glykos & Kokkinidis, 2001)~~. ~~The command script for the solution of the ROP four-helix~~	+	{\|class="wikitable" width=100%
−	~~bundle using the ‘automated MR’ mode of Phaser is shown in Appendix A2.~~ The r.m.s. deviation for ROP is given as 1.0 Å ,since the sequence identity of the polyalanine helix is not a valid estimation of the r.m.s. deviation between the polyalanine helix and the backbone atoms of the ROP structure. The r.m.s. deviation value of 1.0 Å is a reasonable guess. Phaser produces eight solutions after a tree search with hundreds of branches, especially in the search for the second of the four helices. The eight solutions are nearly identical, differing only in the registration of the model to the structure helices (i.e. the Cα residues slip up or down the helix). All eight solutions generate a complete structure after model building with ARP/wARP ~~(Perrakis et al., 2001)~~. Although many potential solutions are stored in the intermediate stages of the search, the search itself is not computationally intensive.	+	\|+ Crystallographic details
		+	! Parameter !! Value !! Comment
		+	\|-
		+	!Space Group
		+	\| C2 \|\|
		+	\|-
		+	!Unit Cell
		+	\| 92Å 24Å 64Å 90° 130° 90° \|\| small
		+	\|-
		+	!Resolution
		+	\| 2.9Å \|\| average
		+	\|-
		+	!Solvent Content
		+	\| ~50% \|\| average
		+	\|-
		+	!ASU Contents
		+	\| 4×26-residue helix \|\| two helix-turn-helix motifs
		+	\|-
		+	!Model Quality
		+	\| 1.0Å r.m.s. \|\| Estimate - polyalanine helix
		+	\|-
		+	!Anomalous atoms
		+	\| N/A \|\|
		+	\|-
		+	!Wavelength
		+	\| N/A \|\|
		+	\|}
		+
		+	;Story
		+	The A31P mutant of ROP forms a helix–turn–helix motif that homodimerizes to form a four-helix bundle. The asymmetric unit contains two copies of the helix–turn–helix motif. The structure was originally solved with a 26-residue polyalanine single helix as the model and an extremely computationally intensive 23- dimensional Monte-Carlo search implemented in the program Queen of Spades.
		+
		+	The r.m.s. deviation for ROP is given as 1.0 Å, since the sequence identity of the polyalanine helix is not a valid estimation of the r.m.s. deviation between the polyalanine helix and the backbone atoms of the ROP structure. The r.m.s. deviation value of 1.0 Å is a reasonable guess.
		+
		+	Phaser produces eight solutions after a tree search with hundreds of branches, especially in the search for the second of the four helices. The eight solutions are nearly identical, differing only in the registration of the model to the structure helices (i.e. the Cα residues slip up or down the helix). All eight solutions generate a complete structure after model building with ARP/wARP. Although many potential solutions are stored in the intermediate stages of the search, the search itself is not computationally intensive.
		+
		+
		+	;Keyword script(s)
		+	<pre>
		+	MODE MR_AUTO
		+	HKLIN beta_blip.mtz
		+	LABIN F=Fobs SIGF=Sigma
		+	ENSEMBLE BETA PDB beta.pdb ID 100
		+	ENSEMBLE BLIP PDB blip.pdb ID 100
		+	SEARCH ENSEMBLE BETA
		+	SEARCH ENSEMBLE BLIP
		+	</pre>
		+
		+	;Reference(s)
		+	:[http://antarctic/phaserwiki/images/4/40/Ba5095.pdf Solving structures of protein complexes by molecular replacement with Phaser ]
		+	:McCoy AJ
		+	:Acta Cryst. (2007). D63, 32-41