fxac mbp 2l and fxac sumo 1l Terrific broth purification 31 oct

FXAC MBP and FXAC pet28 SUMO (BAW, E1, E2, BAE)

FXAC MBP run 2: Run 1 had a nice peak of 250 mAU but lost sample as tubes were not kept in the fraction collector. So I collected the spillage and concentrated to 10ml and injected again to get this small peak. Precipitation was also observed after spillage

FXAC MBP run 3 Third elution was done with 400mM Maltose in 5ml total volume. There was not much protein left in the beads. 

fxacpet28sumo fplc (below curve) fractions A4 to A11

FXAC pet28 SUMO : 10ml of elution from yesterday was injected in the early morning. There was a huge peak of 300 for imidazole in the 120ml range.

sds gel of spherulite from index 46

Additive screen Index 46 spherulites optimization

FXAC MBP Index 46 optimization 5% PEG gave large spherulites

Additive screen and 23 Mocr crystals checked 22Oct

23 CF homology search in PDB

====================================================================

>4IYB:A|PDBID|CHAIN|SEQUENCE

STQVSSGQTYKITNVKAGTVIDLSGEDNKSIIGYPYHSGKNQQWTFNWTGKAWTLRSASSGSYLGIEGTPADGTRLVAVNDPFEWHIWRDEANENAFRIFVPFTNYNLDLSGYGDTTPGTPVQLWWTWEGLHQTWTIDRP

Macrolepiota procera ricin B-like lectin (MPL) in complex with galactose

• DOI: 10.2210/pdb4iyb/pdb

• Classification: SUGAR BINDING PROTEIN
• Deposited: 2013-01-28 Released: 2013-11-20
• Deposition author(s): Renko, M., Zurga, S., Sabotic, J., Pohleven, J., Kos, J., Turk, D.
• Organism: Macrolepiota procera
• Expression System: Escherichia coli

Color key for alignment scores

<40

40-50

50-80

80-200

>=200

Query

1

40

80

120

160

200

Alignments

DownloadGraphics

Sort by:  E value  Score Percent identity Query start position Subject start position 

NextPreviousDescriptions

4IYB:A|PDBID|CHAIN|SEQUENCE

Sequence ID: Query_56515Length: 140Number of Matches: 2

Related Information

Range 1: 6 to 81GraphicsNext MatchPrevious Match

Alignment statistics for match #1

Score	Expect	Method	Identities	Positives	Gaps
19.6 bits(39)	0.017	Compositional matrix adjust.	22/81(27%)	37/81(45%)	9/81(11%)

Query  65   SKKCYKITHVATGKSMTSSEVFNATTKAKYATVSSNPPANFLWTMEPSYGGVNYIQNANT  124
            S + YKIT+V  G  +  S   N +          N    F WT     G    +++A++
Sbjct  6    SGQTYKITNVKAGTVIDLSGEDNKSIIGYPYHSGKNQQWTFNWT-----GKAWTLRSASS  60

Query  125  LEFLKAD---SNGTRL-ALNE  141
              +L  +   ++GTRL A+N+
Sbjct  61   GSYLGIEGTPADGTRLVAVND  81

Range 2: 102 to 106GraphicsNext MatchPrevious MatchFirst Match

Alignment statistics for match #2

Score	Expect	Method	Identities	Positives	Gaps
15.8 bits(29)	0.36	Compositional matrix adjust.	5/5(100%)	5/5(100%)	0/5(0%)

Query  190  PFTNY  194
            PFTNY
Sbjct  102  PFTNY  106

=====================================================================

>5E1H:A|PDBID|CHAIN|SEQUENCE QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGY RAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTL ARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYD VSILIPIIALMVYRCAPP

5E1H:A|PDBID|CHAIN|SEQUENCE

Sequence ID: Query_94813Length: 258Number of Matches: 1

Related Information

Range 1: 186 to 222GraphicsNext MatchPrevious Match

Alignment statistics for match #1

Score	Expect	Method	Identities	Positives	Gaps
15.8 bits(29)	0.76	Compositional matrix adjust.	12/39(31%)	22/39(56%)	3/39(7%)

Query  90   TKAKYATVSSNPPANFLWTMEPSYGGVN-YIQNANTLEF  127
            T+ +Y   S+  P+  + T+E S+G ++  IQ +N   F
Sbjct  186  TRIRYNRRSAPDPS--VITLENSWGRLSTAIQESNQGAF  222

Ricin toxin in complex with neutralizing single chain monoclonal antibodies (VHHs)

Rudolph, M.J., Vance, D., Shoemaker, C., Mantis, N.

To Be Published



===================================================================================

>2AAI:A|PDBID|CHAIN|SEQUENCE
IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF

Crystallographic refinement of ricin to 2.5 A.

Rutenber, E., Katzin, B.J., Ernst, S., Collins, E.J., Mlsna, D., Ready, M.P., Robertus, J.D.

(1991) Proteins 10: 240-250

• PubMed: 1881880 Search on PubMed
• DOI: 10.1002/prot.340100308

PubMed Abstract:

The plant cytotoxin ricin consists of two disulfide-linked chains, each of about 30,000 daltons. An initial model based on a 2.8 A MIR electron density map has been refined against 2.5 A data using rounds of hand rebuilding coupled with  

unnamed protein product

Sequence ID: Query_244321Length: 267Number of Matches: 1

Related Information

Range 1: 190 to 226GraphicsNext MatchPrevious Match

Alignment statistics for match #1

Score	Expect	Method	Identities	Positives	Gaps
15.8 bits(29)	0.83	Compositional matrix adjust.	12/39(31%)	22/39(56%)	3/39(7%)

Query  90   TKAKYATVSSNPPANFLWTMEPSYGGVN-YIQNANTLEF  127
            T+ +Y   S+  P+  + T+E S+G ++  IQ +N   F
Sbjct  190  TRIRYNRRSAPDPS--VITLENSWGRLSTAIQESNQGAF  226

Distribution of 1 Blast Hits on the Query Sequence 

Mouse over to see the title, click to show alignments

Color key for alignment scores

<40

40-50

50-80

80-200

>=200

Query

1

40

80

120

160

200

23CF closest homology paper 4 - mushroom lectin from Marasmius oreades

23CF closest homology paper 3 - neurotoxin

23 CF closest homology paper 2 - mushroom lectin