[ccp4bb] Defining consensus pattern for searching a motif in protein database(s)

Dear All I want to search SUMO interacting motif (SIM) in different protein data bases and also in the given protein sequences. Does anyone can provide me the PROSITE AC and/or ID for the SIM motif?  I will be grateful if you provide me MATRIX for the SIM motif profile. I do not know much about

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[ccp4bb] Purification using GST column at low pH

Dear All Sorry for non-crystallography question. I am purifying a protein using GST column. The gel filtration chromatography is indicating that the protein is aggregating at pH more than 7.0. I am planning to purify the protein at the pH around 6.0. So, I want to know the affinity of GST-fusion

[ccp4bb] 5-methy 2-deoxy Cytidine modified DNA duplex

Dear CCP4 users Sorry for non CCP4 topic. I want to know a company which can synthesize 5-methyl 2-deoxy Cytidine modified DNA duplex. Thank you in advance Rajakumara E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY

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Dear All Sorry for non-crystallography question. I have synthesized two complementary strands of 16 bases in length for making duplex DNA and co-crystallization with DNA binding protein. I have mixed two complementary strands of 1:1 molar ratio (0.5 mM) in water and concentrated to 1.5 mM

[ccp4bb] query on DNA-protein complex preparation for crystallization

Dear All Sorry for non-crystallography question. I have synthesized two complementary strands of 16 bases in length for making duplex DNA and co-crystallization with DNA binding protein. I have mixed two complementary strands of 1:1 molar ratio (0.5 mM) in water and concentrated to 1.5 mM

Re: [ccp4bb] query on DNA-protein complex preparation for crystallization

you can prepare DNA-protein complexes in a variety of ways, including direct addition, concentration, counterdialysis, etc. Regards, Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of E rajakumar Sent: Saturday, June 21, 2008 5:48 PM

Re: [ccp4bb] query on DNA-protein complex preparation for crystallization

, E rajakumar wrote: Hi Artem Evdokimov Thank you for the mail. I have synthesized DMT-on oligos in our laboratory. Deprotection was performed treating with ammonium hydroxide for 15 hours at 55C. Then, DMT-on oligo was separated from off using RPHPLC. DMT was cleaved by treating

[ccp4bb] Ammonium citrate tribasic buffer

Dear All Sorry for non crystallographic query. Can any body mail me how to prepare Ammonium citrate tribasic (citric acid triammonium salt) buffer pH 6.7 to 7.25 and also what is the pKa value. Thanking you in advance Rajakumara E. Rajakumara Postdoctoral Fellow Strcutural Biology Program

[ccp4bb] Query on program for creating random crystallization screen

Dear All I want to create a random crystallization screen using given set of crystallization parameters (pH, Precipitant, salt, additive.) for protein-DNA complex crystallization. I was using Brent Segelke's CRYSTOOL program, not accessible online now. Please can you suggest any other such

[ccp4bb] Protein-DNA complex prepartion for crystallization

Dear All Sorry for non-crystallography query. I am working on DNA binding protein, while mixing DNA with protein for preparing Protein-DNA complex for crystallization, protein is precipitating. pI of the protein is 9.3 and in 15 mM HEPES 7.0, 150mM NaCl and 5% glycerol. Concentration of the

[ccp4bb] Cryoprotectant for protein-DNA complex crystal

Dear All I am working on protein-DNA complex crystals for data collection. These crystals are grown in 15-20 % of PEG3350 or PEG4000 with pH of 6 to 7. When I soak the crystals more than a minute in the cryo solution (15-20% of Glycerol or ethylenglycol + reservoir) the resolution of diffraction

[ccp4bb] Error message while refining protein-DNA complex structure in Refmac5

Dear All I am refining proitein-DNA complex structure in Refamac5. When I used coordinate file containing 2 bases less, then the refinement is running smoth and perfect. But when I built 2 exta bases to the existing DNA in the coot then refinement is failed with the following error message.

Re: [ccp4bb] Error message while refining protein-DNA complex structure in Refmac5

. Could you please remove SCALE lines from the pdb and try again. If it does not help then could you please send me your pdb file and I will try to sort out. Garib On 16 Mar 2009, at 22:43, E rajakumar wrote: Dear All I am refining proitein-DNA complex structure in Refamac5. When I

[ccp4bb] Error message while refining protein-DNA complex structure in Refmac5

remove SCALE lines from the pdb and try again. If it does not help then could you please send me your pdb file and I will try to sort out. Garib On 16 Mar 2009, at 22:43, E rajakumar wrote: Dear All I am refining proitein-DNA complex structure in Refamac5. When I used coordinate

[ccp4bb] Question on calculation of RMSD

Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in

Re: [ccp4bb] how to quantitate protein which dont have ne aromatic residue

Hi Arpita You can try QUANTI-iT Protein assay kit from Invitrogen. But still there is nearly 20-50% discrepancy between this method and a Abosorbance at 280. I also faced same problem with a protein, then re-cloned by adding a Trp at the C-terminus. Raj   E. Rajakumara Postdoctoral Fellow

[ccp4bb] Protein crystallizes while concentration

Dear All I am Rajkumar, working on the protein which has unusual behavior while concentration. When I kept protein in 15 mM Tris 7.5, 150 mM NaCl and 5 mM DTT, the solubility of the protein is decreases drastically and tend to crystallize while concentration. Protein cannot be concentrated