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Acyl-Acyl Carrier Protein (PDB 2FAE)

by MoleculeMaker, published

Acyl-Acyl Carrier Protein (PDB 2FAE) by MoleculeMaker Jun 23, 2013
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3101Views 508Downloads Found in Biology

Summary

I recently painted this and added some additional photos. If you are going to attempt to print one of my protein models, this is probably the best one to start with, as it has supports built in.

This is a model of the structure of Escherichia coli decanoyl-Acyl Carrier Protein. The model is based on the crystal structure and the PDB file 2FAE.

This printed well, and is now a completed model.

This protein is from the common bacterium E. coli, and is important for moving around lipid molecules (oils) within the cell.. It has a decanoyl (C10 fatty acid) group attached to the cofactor, which I have represented as CPK, along with the sidechain ligand. It is actually quite a robust structure, but is able to flex quite a bit..

Instructions

This structure is an extensive print. It takes about 5 hours to print it. I printed mine with a raft, but it does not require any supports, as I have built in my own, which are very easy to remove. In fact, I removed my supports in about 10 minutes with a needle nose pliar, and spent another 20 minutes trimming it off with a hobby knife, and it looks great. I am printing at medium quality. I printed this out on a Makerbot Replicator 2.

The model took a good deal of effort to construct. The original pdb file (2FAE) was manipulated until only the single monomer with no water molecules was included. This was then placed into the program VMD. I manipulated the backbone as cartoons, and then selected the cofactor and sidechain for display as CPK. This was then imported in several segments into tinkercad (tinkercad had a problem importing files larger than 20 Mb, so I had to import and then align as three components. I then grouped and aligned everything, and added a number of manual support features at the bottom. All of the supports are designed to be removed.

I spent a lot of time building the support structure to make it easy to remove and provide a much cleaner print than some of my previous protein models. I'm not going to work on something a little bit bigger and more complex.

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Hi Brett! Nice looking molecules! A couple questions: 1) When I downloaded the STL file it had godzillion of errors (resulting in holes in the shell visible in slic3r) - I bet you don't have them and wonder if you could point out where they could be coming from. 2) Have you tried to print surface representations - if so, did you manage to get the bottom part (facing the support material) to be as smooth as the top?
Thanks!

I just downloaded the stl file into makerware again to check on it, and it looks fine. There are small support beams that I put in throughout. These help it to print and then are removed at the end. I'm not sure what you are talking about with the holes in the visible shell. You can see an image of what the file looks like on the 4th image over. Not sure why you are having a problem with the stl file. I could send you a x3g version as well, but it has been posted for some time, and I've never heard of anyone having issues with my models before. I could also send you a version through tinkercad (I think I still have this file available). What model of makerbot are you using.

Sorry I can't be more help.

Thank you for the reply. It seems it is a Slic3r specific problem. In netfabb and UCSF Chimera it opens fine. Could you answer my question on printing surface representation of the molecules (above)? Thanks!

I'm not sure what you mean by printing a surface representation. The file is a .stl file. Once I complete these (I do the final version in tinkercad to fix any errors and add the supports), I simply transfer it to the makerbot software and turn it into an .x3g file. I have also produced .gcode files so I can look at how each layer prints to look for errors. There is always some roughness on the bottom where the supports are (see the images I posted). I minimize these through the supports, and do get relatively smooth surfaces throughout. This print is actually quite robust. I just got a newer Makerbot Replicator (5th generation), and will try to print it out on that as well soon. Sorry to hear that you are having such issues with it. If you send me a message, I can give you my phone number, and we could talk about this directly, if that would help. I feel like I'm not answering your question.

Appreciate your answer. I meant surface representation of molecules in general (not of this particular case). Here you have "cartoon" representation. I meant something like this: https://bionano.cent.uw.edu.pl/Software/SurfaceDiver/UsersManual/Surface.
If you could shoot me an email to bazilione at gmail dot com I will send you the image of the problem I have with the bottom surface. Thanks!

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