Difference between revisions of "Part:BBa K2740016"

 
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<partinfo>BBa_K2740016 parameters</partinfo>
 
<partinfo>BBa_K2740016 parameters</partinfo>
 
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Parameter of Protein
 +
 +
Number of amino acids: 453
 +
 +
Molecular weight: 49636.54
 +
 +
Theoretical pI: 6.00
 +
 +
Amino acid composition:
 +
Ala (A)  39   8.6%
 +
Arg (R)  29   6.4%
 +
Asn (N)  11   2.4%
 +
Asp (D)  19   4.2%
 +
Cys (C)  7   1.5%
 +
Gln (Q)  16   3.5%
 +
Glu (E)  37   8.2%
 +
Gly (G)  45   9.9%
 +
His (H)  10   2.2%
 +
Ile (I)    30   6.6%
 +
Leu (L)  38   8.4%
 +
Lys (K)  21   4.6%
 +
Met (M)  11   2.4%
 +
Phe (F)  12   2.6%
 +
Pro (P)  21   4.6%
 +
Ser (S)  32   7.1%
 +
Thr (T)  24   5.3%
 +
Trp (W)  6   1.3%
 +
Tyr (Y)  15   3.3%
 +
Val (V)  30   6.6%
 +
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): 56
 +
Total number of positively charged residues (Arg + Lys): 50
 +
 +
Atomic composition:
 +
 +
Carbon      C       2192
 +
Hydrogen    H       3480
 +
Nitrogen    N       614
 +
Oxygen      O       664
 +
Sulfur      S         18
 +
 +
Formula: C2192H3480N614O664S18
 +
Total number of atoms: 6968
 +
 +
Extinction coefficients:
 +
 +
Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
 +
 +
Ext. coefficient    55725
 +
Abs 0.1% (=1 g/l)  1.123, assuming all pairs of Cys residues form cystines
 +
 +
 +
Ext. coefficient    55350
 +
Abs 0.1% (=1 g/l)  1.115, 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 40.63
 +
This classifies the protein as unstable.
 +
 +
 +
 +
Aliphatic index: 86.36
 +
 +
Grand average of hydropathicity (GRAVY): -0.234
 +
 +
Design Notes
 +
Nitrogenase is a complex enzyme system consisting of nine protein components. Additionally, to maintain stoichiometry of these protein components is an essential requirement for nitrogenase biosynthesis and activity. However, there is only one copy of each structure gene present in the nif gene cluster. Therefore, cloning each of these nif genes and setting as independent part can facilitate the regulation of balancing expression ratios from the transcription and/or translation level(s) when they are heterogeneously expressed in non-diazotrophic hosts.We sent the sequences of the PCR template to synthesis, but unfortunately, EcoRI and PstI striction enzyme cut site was involved after they promoted it again. But the part can be manipulated by XbaI and SpeI or can be assembled by gibson assembly,that is what we did.

Revision as of 05:30, 4 October 2018


CR1 nifE

CR1 nifE encodes the cofactor NifE for the maturation of functional molybdenum-iron protein.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 6
    Illegal AgeI site found at 379
  • 1000
    COMPATIBLE WITH RFC[1000]


Parameter of Protein

Number of amino acids: 453

Molecular weight: 49636.54

Theoretical pI: 6.00

Amino acid composition: Ala (A) 39 8.6% Arg (R) 29 6.4% Asn (N) 11 2.4% Asp (D) 19 4.2% Cys (C) 7 1.5% Gln (Q) 16 3.5% Glu (E) 37 8.2% Gly (G) 45 9.9% His (H) 10 2.2% Ile (I) 30 6.6% Leu (L) 38 8.4% Lys (K) 21 4.6% Met (M) 11 2.4% Phe (F) 12 2.6% Pro (P) 21 4.6% Ser (S) 32 7.1% Thr (T) 24 5.3% Trp (W) 6 1.3% Tyr (Y) 15 3.3% Val (V) 30 6.6% 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): 56 Total number of positively charged residues (Arg + Lys): 50

Atomic composition:

Carbon C 2192 Hydrogen H 3480 Nitrogen N 614 Oxygen O 664 Sulfur S 18

Formula: C2192H3480N614O664S18 Total number of atoms: 6968

Extinction coefficients:

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

Ext. coefficient 55725 Abs 0.1% (=1 g/l) 1.123, assuming all pairs of Cys residues form cystines


Ext. coefficient 55350 Abs 0.1% (=1 g/l) 1.115, 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 40.63 This classifies the protein as unstable.


Aliphatic index: 86.36

Grand average of hydropathicity (GRAVY): -0.234

Design Notes Nitrogenase is a complex enzyme system consisting of nine protein components. Additionally, to maintain stoichiometry of these protein components is an essential requirement for nitrogenase biosynthesis and activity. However, there is only one copy of each structure gene present in the nif gene cluster. Therefore, cloning each of these nif genes and setting as independent part can facilitate the regulation of balancing expression ratios from the transcription and/or translation level(s) when they are heterogeneously expressed in non-diazotrophic hosts.We sent the sequences of the PCR template to synthesis, but unfortunately, EcoRI and PstI striction enzyme cut site was involved after they promoted it again. But the part can be manipulated by XbaI and SpeI or can be assembled by gibson assembly,that is what we did.