Difference between revisions of "Part:BBa K1080006:Design"

 
(→‎Design Notes)
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===Design Notes===
 
===Design Notes===
−
Incorporated sequence overlap for Gibson assembly and no GC rich regions or restriction sites within sequence
+
Incorporated sequence overlap for Gibson assembly and no GC rich regions or restriction sites within sequence.
  
 +
<b>Amino acid sequence</b>
  
 +
<FONT FACE="courier">MATVKLGADS GALEFVPKTL TIKSGETVNF VNNAGFPHNI VFDEDAIPSG VNADAISRDD<br> YLNAPGETYS VKLTAAGEYG YYCEPHQGAG MVGKIIVQ </FONT> 
 +
 +
References and documentation are available.
 +
Please note the modified algorithm for extinction coefficient.
 +
 +
--------------------------------------------------------------------------------
 +
Number of amino acids: 98
 +
 +
Molecular weight: 10339.5
 +
 +
Theoretical pI: 4.57
 +
 +
Amino acid composition: Ala (A)  11 11.2%
 +
Arg (R)  1   1.0%
 +
Asn (N)  6   6.1%
 +
Asp (D)  6   6.1%
 +
Cys (C)  1   1.0%
 +
Gln (Q)  2   2.0%
 +
Glu (E)  6   6.1%
 +
Gly (G)  11 11.2%
 +
His (H)  2   2.0%
 +
Ile (I)  6   6.1%
 +
Leu (L)  5   5.1%
 +
Lys (K)  5   5.1%
 +
Met (M)  2   2.0%
 +
Phe (F)  4   4.1%
 +
Pro (P)  5   5.1%
 +
Ser (S)  5   5.1%
 +
Thr (T)  6   6.1%
 +
Trp (W)  0   0.0%
 +
Tyr (Y)  5   5.1%
 +
Val (V)  9   9.2%
 +
Pyl (O)  0   0.0%
 +
Sec (U)  0   0.0%
 +
 +
(B)  0   0.0%
 +
(Z)  0   0.0%
 +
(X)  0   0.0%
 +
 +
 +
Total number of negatively charged residues (Asp + Glu): 12
 +
Total number of positively charged residues (Arg + Lys): 6
 +
 +
Atomic composition:
 +
 +
Carbon      C       460
 +
Hydrogen    H       708
 +
Nitrogen    N       118
 +
Oxygen      O       147
 +
Sulfur      S         3
 +
 +
Formula: C460H708N118O147S3
 +
Total number of atoms: 1436
 +
 +
Extinction coefficients:
 +
 +
This protein does not contain any Trp residues. Experience shows that
 +
this could result in more than 10% error in the computed extinction coefficient.
 +
 +
Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
 +
 +
Ext. coefficient    7450
 +
Abs 0.1% (=1 g/l)  0.721, assuming all pairs of Cys residues form cystines
 +
 +
 +
Ext. coefficient    7450
 +
Abs 0.1% (=1 g/l)  0.721, assuming all Cys residues are reduced
 +
 +
Estimated half-life:
 +
 +
The N-terminal of the sequence considered is M (Met).
 +
 +
The estimated half-life is:
 +
                            30 hours (mammalian reticulocytes, in vitro).
 +
                            >20 hours (yeast, in vivo).
 +
                            >10 hours (Escherichia coli, in vivo).
 +
 +
 +
Instability index:
 +
 +
The instability index (II) is computed to be 18.58
 +
This classifies the protein as stable.
 +
 +
 +
 +
Aliphatic index: 81.63
 +
 +
Grand average of hydropathicity (GRAVY): -0.065
  
 
===Source===
 
===Source===

Revision as of 10:38, 25 September 2013


Plastocyanin


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 100
    Illegal BsaI.rc site found at 223


Design Notes

Incorporated sequence overlap for Gibson assembly and no GC rich regions or restriction sites within sequence.

Amino acid sequence

MATVKLGADS GALEFVPKTL TIKSGETVNF VNNAGFPHNI VFDEDAIPSG VNADAISRDD
YLNAPGETYS VKLTAAGEYG YYCEPHQGAG MVGKIIVQ

References and documentation are available. Please note the modified algorithm for extinction coefficient.

Number of amino acids: 98

Molecular weight: 10339.5

Theoretical pI: 4.57

Amino acid composition: Ala (A) 11 11.2% Arg (R) 1 1.0% Asn (N) 6 6.1% Asp (D) 6 6.1% Cys (C) 1 1.0% Gln (Q) 2 2.0% Glu (E) 6 6.1% Gly (G) 11 11.2% His (H) 2 2.0% Ile (I) 6 6.1% Leu (L) 5 5.1% Lys (K) 5 5.1% Met (M) 2 2.0% Phe (F) 4 4.1% Pro (P) 5 5.1% Ser (S) 5 5.1% Thr (T) 6 6.1% Trp (W) 0 0.0% Tyr (Y) 5 5.1% Val (V) 9 9.2% Pyl (O) 0 0.0% Sec (U) 0 0.0% 

(B)   0	  0.0%
(Z)   0	  0.0%
(X)   0	  0.0%


Total number of negatively charged residues (Asp + Glu): 12 Total number of positively charged residues (Arg + Lys): 6

Atomic composition:

Carbon C 460 Hydrogen H 708 Nitrogen N 118 Oxygen O 147 Sulfur S 3

Formula: C460H708N118O147S3 Total number of atoms: 1436

Extinction coefficients:

This protein does not contain any Trp residues. Experience shows that this could result in more than 10% error in the computed extinction coefficient.

Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.

Ext. coefficient 7450 Abs 0.1% (=1 g/l) 0.721, assuming all pairs of Cys residues form cystines


Ext. coefficient 7450 Abs 0.1% (=1 g/l) 0.721, assuming all Cys residues are reduced

Estimated half-life:

The N-terminal of the sequence considered is M (Met).

The estimated half-life is: 

                            30 hours (mammalian reticulocytes, in vitro).
                           >20 hours (yeast, in vivo).
                           >10 hours (Escherichia coli, in vivo).


Instability index:

The instability index (II) is computed to be 18.58 This classifies the protein as stable.


Aliphatic index: 81.63

Grand average of hydropathicity (GRAVY): -0.065

Source

From genome of Chlamydomonas reinhardtii

References