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This gene has the annotation "similar to NifU protein".
The target was selected as part of JMC's third set.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | jmc | 2002-11-07 |
| Cloned | Done | r_kim | 2003-02-11 |
| Expression tested | Done | r_kim | 2003-02-11 |
| Solubility tested | S | r_kim | 2003-02-11 |
| Purified | Done | dhshin | 2003-05-28 |
| Crystallized | Done | dhshin | 2003-05-28 |
| Diffraction quality crystals | Done | dhshin | 2003-05-28 |
| Native diffraction data | Done | dhshin | 2003-05-28 |
| Phasing diffraction data | Done | dhshin | 2003-07-07 |
| Traceable map | Done | dhshin | 2003-07-07 |
| Crystal structure | Done | dhshin | 2003-08-29 |
| In PDB | 1SU0 | dhshin | 2004-03-26 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP354 / MPN488 | -19.22 | 22.63 | 86.16 |
ATGGCACTCTCTAAACTGAACCATCTATACATGGCTGTGGTAGCGGACCATTCGAAACGTCCACATCATCATGGGCAACT AGATGGCGTAGAGGCTGTTCAACTGAATAATCCGACTTGTGGTGATGTGATTTCTTTGACCGTTAAGTTTGACGAAGATA AAATTGAAGATATTGCTTTTGCAGGCAACGGCTGTACCATTTCCACAGCTTCATCAAGCATGATGACAGATGCTGTTATT GGTAAAAGTAAAGAAGAAGCACTCGCGTTAGCTGATATTTTTTCAGAGATGGTACAAGGACAGGAAAATCCTGCTCAAAA AGAGCTAGGTGAAGCAGAATTGTTGGCAGGAGTTGCAAAATTTCCACAGCGTATCAAATGCTCTACCCTAGCTTGGAATG CTCTCAAGGAAGCCATTAAACGAAGTGCCAATGCTCAGCACCTCACGGACCAAAATGTAAAGGAAGGGAAAAATGTCTGA
(160 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU25.0( 4) UCU18.8( 3) UAU0.0( 0) UGU12.5( 2) UUC0.0( 0) UCC6.2( 1) UAC6.2( 1) UGC6.2( 1) UUA6.2( 1) UCA18.8( 3) UAA0.0( 0) UGA6.2( 1) UUG18.8( 3) UCG6.2( 1) UAG0.0( 0) UGG6.2( 1) CUU0.0( 0) CCU6.2( 1) CAU31.2( 5) CGU12.5( 2) CUC25.0( 4) CCC0.0( 0) CAC6.2( 1) CGC0.0( 0) CUA25.0( 4) CCA12.5( 2) CAA31.2( 5) CGA6.2( 1) CUG12.5( 2) CCG6.2( 1) CAG18.8( 3) CGG0.0( 0) AUU43.8( 7) ACU6.2( 1) AAU43.8( 7) AGU12.5( 2) AUC6.2( 1) ACC18.8( 3) AAC12.5( 2) AGC6.2( 1) AUA0.0( 0) ACA12.5( 2) AAA62.5( 10) AGA0.0( 0) AUG31.2( 5) ACG6.2( 1) AAG18.8( 3) AGG0.0( 0) GUU25.0( 4) GCU62.5( 10) GAU37.5( 6) GGU18.8( 3) GUC6.2( 1) GCC12.5( 2) GAC18.8( 3) GGC18.8( 3) GUA25.0( 4) GCA37.5( 6) GAA56.2( 9) GGA12.5( 2) GUG12.5( 2) GCG12.5( 2) GAG18.8( 3) GGG12.5( 2)
Note: These were generated using Hisao's algorithm, and do not take into account possible mispriming, self-complementarity, or requirements for mutations anywhere in the sequences. The -R1 primers are for the N-terminal end, and begin with an NdeI restriction site (CATATG). The -R2 primers are for the C-terminal end, and begin with a BamHI site (GGATCC) if the target has no other BamHI sites. If the target does have a BamHI site, the -R2 primer wil begin with a BglII site (AGATCT), unless the target has no BglII sites. If the target has both sites, the design program gives up and doesn't prepend a restriction site to the -R2 primer!
Predicted Tm was obtained using the Tm determination tool at the Virtual Genome Center.
| Primer ID | Predicted Tm | sequence |
|---|---|---|
| 1323B-R1 | 60.00 | CATATGGCACTCTCTAAACTGAACCA |
| 1323B-R2 | 60.60 | GGATCCTTAGACATTTTTCCCTTCCTTTACATTT |
| 1323B-R10 | 63.20 | GGCGGTGGTGGCGGCATGGCACTCTCTAAACTGAACCATCTATAC |
| 1323B-R11 | 63.70 | GTTCTTCTCCTTTGCGCCCCTAGACATTTTTCCCTTCCTTTACATTTTG |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atggcactctctaaactgaaccatctatacatggctgtggtagcggaccattcgaaacgt M A L S K L N H L Y M A V V A D H S K R ccacatcatcatgggcaactagatggcgtagaggctgttcaactgaataatccgacttgt P H H H G Q L D G V E A V Q L N N P T C ggtgatgtgatttctttgaccgttaagtttgacgaagataaaattgaagatattgctttt G D V I S L T V K F D E D K I E D I A F gcaggcaacggctgtaccatttccacagcttcatcaagcatgatgacagatgctgttatt A G N G C T I S T A S S S M M T D A V I ggtaaaagtaaagaagaagcactcgcgttagctgatattttttcagagatggtacaagga G K S K E E A L A L A D I F S E M V Q G caggaaaatcctgctcaaaaagagctaggtgaagcagaattgttggcaggagttgcaaaa Q E N P A Q K E L G E A E L L A G V A K tttccacagcgtatcaaatgctctaccctagcttggaatgctctcaaggaagccattaaa F P Q R I K C S T L A W N A L K E A I K cgaagtgccaatgctcagcacctcacggaccaaaatgtaaaggaagggaaaaatgtctga R S A N A Q H L T D Q N V K E G K N V *
MALSKLNHLYMAVVADHSKRPHHHGQLDGVEAVQLNNPTCGDVISLTVKFDEDKIEDIAFAGNGCTISTASSSMMTDAVI GKSKEEALALADIFSEMVQGQENPAQKELGEAELLAGVAKFPQRIKCSTLAWNALKEAIKRSANAQHLTDQNVKEGKNV
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 159
Molecular weight: 17142.4
Theoretical pI: 5.65
Amino acid composition:
Ala (A) 20 12.6%
Arg (R) 3 1.9%
Asn (N) 9 5.7%
Asp (D) 9 5.7%
Cys (C) 3 1.9%
Gln (Q) 8 5.0%
Glu (E) 12 7.5%
Gly (G) 10 6.3%
His (H) 6 3.8%
Ile (I) 8 5.0%
Leu (L) 14 8.8%
Lys (K) 13 8.2%
Met (M) 5 3.1%
Phe (F) 4 2.5%
Pro (P) 4 2.5%
Ser (S) 11 6.9%
Thr (T) 7 4.4%
Trp (W) 1 0.6%
Tyr (Y) 1 0.6%
Val (V) 11 6.9%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 21
Total number of positively charged residues (Arg + Lys): 16
Atomic composition:
Carbon C 742
Hydrogen H 1201
Nitrogen N 211
Oxygen O 238
Sulfur S 8
Formula: C742H1201N211O238S8
Total number of atoms: 2400
Extinction coefficients:
Conditions: 6.0 M guanidium hydrochloride
0.02 M phosphate buffer
pH 6.5
Extinction coefficients are in units of M-1 cm-1 .
The first table lists values computed assuming ALL Cys
residues appear as half cystines, whereas the second table
assumes that NONE do.
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 6995 7127 7125 7090 6920
Abs 0.1% (=1 g/l) 0.408 0.416 0.416 0.414 0.404
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 6850 7000 7005 6970 6800
Abs 0.1% (=1 g/l) 0.400 0.408 0.409 0.407 0.397
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 32.61
This classifies the protein as stable.
Aliphatic index: 86.60
Grand average of hydropathicity (GRAVY): -0.271