Results 5: Difference between revisions
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=FUNCTION= | =FUNCTION= | ||
=EVOLUTION= |
Revision as of 04:45, 11 June 2007
STRUCTURE
Quality of YlqF protein model and overall structure
The asymmetric unit of Bacillus subtilis YlqF protein consists of a polymer containing 282 amino acids (Figure 1). The protein has been refined at 2 angstroms to a crystallographic R factor of 21.6% and free R factor of 25%. Table 1 summarizes the refinement statistics including protein quality parameters. MolProbity Ramachandran analysis of YlqF in shows that 96.5% of all residues lie in the favoured regions and 98.8% of all residues lie in the allowed regions.
Table 1. Crystal parameters and refinement statistics
Parameters | Resolution[Å]
2.00 |
R factor, %
21.6 |
Free R factor, %
25.0 |
Space Group
P 21 21 21 |
Unit Cell | Length[Å]
Angles [°] |
a
alpha |
36.75
90.00 |
b
beta |
68.57
90.00 |
c
gamma |
105.57
90.00 |
---|
1 - MTIQWFPGHM AKARREVTEK LKLIDIVYEL VDARIPMSSR NPMIEDILKN KPRIMLLNKA 61 - DKADAAVTQQ WKEHFENQGI RSLSINSVNG QGLNQIVPAS KEILQEKFDR MRAKGVKPRA 121 - IRALIIGIPN VGKSTLINRL AKKNIAKTGD RPGITTSQQW VKVGKELELL DTPGILWPKF 181 - EDELVGLRLA VTGAIKDSII NLQDVAVFGL RFLEEHYPER LKERYGLDEI PEDIAELFDA 241 - IGEKRGCLMS GGLINYDKTT EVIIRDIRTE KFGRLSFEQP TM
Figure 1. Amino acid sequence of YlqF
The secondary structure of YlqF mainly contains 50% helical (13 helices; 142 residues) and 10% beta sheet (6 strands; 31 residues)(see Figure 2). YlqF protein consists of two domains. One domain contains Rossmann fold with α/β class. This domain possesses 1-177 residues, and forms a 3-layer sandwich structure. The other one is referred to as a conserved hypothetical protein with mainly α class. This possesses 178-282 residues, and forms a orthogonal bundle structure. YlqF is also classified as a signalling protein. The molecular weight of the protein is 31986 Da.
= pi helix,
= 310 helix,
= extended strand,
= turn,
= alpha helix,
Greyed out residues have no structural information
Figure 2. Sequence and Secondary Structure
Structure Analysis
Structure classification of proteins (SCOP) classified YlqF as shown in Table 2. The results of Pfam classification described YlqF as GTPase of unknown function, Rhomboid family, and catalytic domain of alpha amylase.
Class
Alpha and beta proteins |
Fold
P-loop containing nucleoside triphosphate hydrolases |
Superfamily
P-loop containing nucleoside triphosphate hydrolases |
Family
G proteins |
Domain
Probable GTPase YlqF |
Species
Bacillus subtilis |