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Plastocyanin (pdb 2CJ3)

by MoleculeMaker, published

Plastocyanin (pdb 2CJ3) by MoleculeMaker Mar 30, 2013

Description

This is a model of the structure of the electron transport protein plastocyanin. The model is based on the crystal structure and the PDB file 2CJ3.

This printed well, and is now a completed model. I have painted it and provided some pictures.

This protein is found in the cyanobacterium Anabaena variabilis, and is an important component of the electron transport chain. It has a single copper heteroatom, which I have represented as CPK, along with the two histidine and single cysteine ligands.I tried to print this initially as a smaller protein without supports, but it was too flimsy and broke, so I put in some supports and made a larger model, which printed very well. It is quite sturdy. I painted the atoms in standard colors, with the copper painted magenta and the alpha helices in orange and the beta sheets in teal.

Recent Comments

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I printed at Medium Quality using the default settings (10% infill, 2 shells, 0.27 layer height). I included supports, but not a raft (which I later regretted, as it was hard to remove from the base). I started this just after my lunch one overnoon, and then came back at about 9:00 PM, and it was done. I could be remembering this wrong. It is quite a long print, and quite intensive on the PLA that it will use.
Only six hours!? Please, share your feed rate and layer heights.. By my estimate this should take 12 hours at least
About 6 hours with supports (which are required for a successful print) I need to post some pictures to give people an idea of how extensive the support structure is....

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Instructions

This structure is an extensive print. THIS CAN ONLY BE PRINTED WITH SUPPORT selected in Makerware, and a word of warning, expect 2-3 hours to remove the support and get down to the actual model. I had a difficult time removing this from the base, so you might want to include a raft as well. I removed the supports, and have painted it. I am printing at medium quality. The build time was nearly 6 hours, so be warned, it takes some time. This model is sturdy, but you need to be careful to keep the braces intact, so take your time removing the support. I use a pair of needlenose pliars to break off the support structure slowly, and remove the support from the remaining model. I printed this out on a Makerbot Replicator 2.

The model took a good deal of effort to construct. The original pdb file (2CJ3) 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 histidine and cysteine ligands along with the copper heteroatom for display as CPK, and added some bonds to serve as supports to hold the structure together (these are somewhat flimsy). 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. The bottom braces are designed to be removed, while the internal braces hold the model together. I did break a small brace, but glued it back together with some model glue.

If you do choose to print this out, be prepared for a significant level of work, and be patient removing the supports, but the print is very nice. I painted the alpha helices in orange and the beta sheets in teal, and also painted the individual atoms of the copper and ligands.

how long did it take to print this?
About 6 hours with supports (which are required for a successful print) I need to post some pictures to give people an idea of how extensive the support structure is....
Only six hours!? Please, share your feed rate and layer heights.. By my estimate this should take 12 hours at least
I printed at Medium Quality using the default settings (10% infill, 2 shells, 0.27 layer height). I included supports, but not a raft (which I later regretted, as it was hard to remove from the base). I started this just after my lunch one overnoon, and then came back at about 9:00 PM, and it was done. I could be remembering this wrong. It is quite a long print, and quite intensive on the PLA that it will use.
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