Difference between revisions of "Part:BBa K2740012"
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<partinfo>BBa_K2740012 parameters</partinfo> | <partinfo>BBa_K2740012 parameters</partinfo> | ||
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| + | <h2><u>Parameter of Protein</u></h2> | ||
| + | <p align="left"> </p> | ||
| + | <p align="left">Number of amino acids: 499</p> | ||
| + | <p align="left">Molecular weight: 54885.93</p> | ||
| + | <p align="left">Theoretical pI: 7.24</p> | ||
| + | <p align="left">Amino acid composition: <br /> | ||
| + | Ala (A) 45 9.0%<br /> | ||
| + | Arg (R) 35 7.0%<br /> | ||
| + | Asn (N) 18 3.6%<br /> | ||
| + | Asp (D) 23 4.6%<br /> | ||
| + | Cys (C) 16 3.2%<br /> | ||
| + | Gln (Q) 19 3.8%<br /> | ||
| + | Glu (E) 38 7.6%<br /> | ||
| + | Gly (G) 42 8.4%<br /> | ||
| + | His (H) 17 3.4%<br /> | ||
| + | Ile (I) 29 5.8%<br /> | ||
| + | Leu (L) 41 8.2%<br /> | ||
| + | Lys (K) 26 5.2%<br /> | ||
| + | Met (M) 12 2.4%<br /> | ||
| + | Phe (F) 13 2.6%<br /> | ||
| + | Pro (P) 25 5.0%<br /> | ||
| + | Ser (S) 28 5.6%<br /> | ||
| + | Thr (T) 16 3.2%<br /> | ||
| + | Trp (W) 2 0.4%<br /> | ||
| + | Tyr (Y) 13 2.6%<br /> | ||
| + | Val (V) 41 8.2%<br /> | ||
| + | Pyl (O) 0 0.0%<br /> | ||
| + | Sec (U) 0 0.0%</p> | ||
| + | <p align="left"> (B) 0 0.0%<br /> | ||
| + | (Z) 0 0.0%<br /> | ||
| + | (X) 0 0.0%</p> | ||
| + | <p align="left"> </p> | ||
| + | <p align="left">Total number of negatively charged residues (Asp + Glu): 61<br /> | ||
| + | Total number of positively charged residues (Arg + Lys): 61</p> | ||
| + | <p align="left">Atomic composition:</p> | ||
| + | <p align="left">Carbon C 2398<br /> | ||
| + | Hydrogen H 3853<br /> | ||
| + | Nitrogen N 703<br /> | ||
| + | Oxygen O 716<br /> | ||
| + | Sulfur S 28</p> | ||
| + | <p align="left">Formula: C2398H3853N703O716S28<br /> | ||
| + | Total number of atoms: 7698</p> | ||
| + | <p align="left">Extinction coefficients:</p> | ||
| + | <p align="left">Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.</p> | ||
| + | <p align="left">Ext. coefficient 31370<br /> | ||
| + | Abs 0.1% (=1 g/l) 0.572, assuming all pairs of Cys residues form cystines</p> | ||
| + | <p align="left"> </p> | ||
| + | <p align="left">Ext. coefficient 30370<br /> | ||
| + | Abs 0.1% (=1 g/l) 0.553, assuming all Cys residues are reduced</p> | ||
| + | <p align="left">Estimated half-life:</p> | ||
| + | <p align="left">The N-terminal of the sequence considered is M (Met).</p> | ||
| + | <p align="left">The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).<br /> | ||
| + | >20 hours (yeast, in vivo).<br /> | ||
| + | >10 hours (Escherichia coli, in vivo).</p> | ||
| + | <p align="left"> </p> | ||
| + | <p align="left">Instability index:</p> | ||
| + | <p align="left">The instability index (II) is computed to be 43.00<br /> | ||
| + | This classifies the protein as unstable.</p> | ||
| + | <p align="left"> </p> | ||
| + | <p align="left">Aliphatic index: 87.56</p> | ||
| + | <p align="left">Grand average of hydropathicity (GRAVY): -0.254</p> | ||
| + | <div> | ||
| + | <h2>Design Notes</h2> | ||
| + | </div> | ||
| + | <p align="left">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.</p> | ||
Revision as of 05:16, 4 October 2018
CR1 nifB
CR1 nifB encodes nitrogen fixation protein NifB that is essential for biosynthesis of the active-site nitrogenase cofactor. If the CR1 nifB was deleted, the nitrogen fixation would not happen.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Parameter of Protein
Number of amino acids: 499
Molecular weight: 54885.93
Theoretical pI: 7.24
Amino acid composition:
Ala (A) 45 9.0%
Arg (R) 35 7.0%
Asn (N) 18 3.6%
Asp (D) 23 4.6%
Cys (C) 16 3.2%
Gln (Q) 19 3.8%
Glu (E) 38 7.6%
Gly (G) 42 8.4%
His (H) 17 3.4%
Ile (I) 29 5.8%
Leu (L) 41 8.2%
Lys (K) 26 5.2%
Met (M) 12 2.4%
Phe (F) 13 2.6%
Pro (P) 25 5.0%
Ser (S) 28 5.6%
Thr (T) 16 3.2%
Trp (W) 2 0.4%
Tyr (Y) 13 2.6%
Val (V) 41 8.2%
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): 61
Total number of positively charged residues (Arg + Lys): 61
Atomic composition:
Carbon C 2398
Hydrogen H 3853
Nitrogen N 703
Oxygen O 716
Sulfur S 28
Formula: C2398H3853N703O716S28
Total number of atoms: 7698
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 31370
Abs 0.1% (=1 g/l) 0.572, assuming all pairs of Cys residues form cystines
Ext. coefficient 30370
Abs 0.1% (=1 g/l) 0.553, 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 43.00
This classifies the protein as unstable.
Aliphatic index: 87.56
Grand average of hydropathicity (GRAVY): -0.254
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.