Re: [ccp4bb] Unknown density in Trypsin

Dear Mahmoud, The first thing to do is to make a list of (a) all your protein buffer components, (b) all your crystallisation conditions components, and (c) all the cryo-protection chemicals, and try to consider all of those as possibilities, but then again indeed it is most likely glycerol

Re: [ccp4bb] unknown density in 1.6 A structure

Dear Nick, I like your idea and your comments on this substance. 1,2-hexandiol supposed to be chiral but probably it is used as a racemic mixture in cosmetics. There is even a crystal structure in the PDB (4EUS) and an associated 3 letter code. I´ll give it a try because it seems to fit

Re: [ccp4bb] unknown density in 1.6 A structure

Hi Peer, Reminds me of a lipocalin structure I solved which co-purified fatty acid with it. I could model fatty acids and we along with our collaborators used several complementary biophysical methods followed by functional assays to identify the ligand.

Re: [ccp4bb] unknown density in 1.6 A structure

Dear Peer, This reminds me of my colleague Michael Rossmann's discovery of a Pocket Factor which is a fatty acid-like molecule residing in a hydrophobic pocket underneath the "canyon" in enteroviruses. See https://link.springer.com/article/10.1007/s13238-014-0092-6. You likely have an endogenous

Re: [ccp4bb] unknown density in 1.6 A structure

Hi Peer, If I understand you correctly you are saying that you do not know what substance may be in the density; then perhaps you only need to extend by an extra atom to create a new kind of symmetrical molecule that will fit the density? BW, D On 03/06/2021 11:55, SHEPARD William wrote:

Re: [ccp4bb] unknown density in 1.6 A structure

Hi Peer, Have you tried to model the hydroxyl O1 disordered at the carbonyl position? Check the H-bonding pattern to the end groups, this might give some clues. Cheers, Bill Le 03/06/21 12:50, « Peer Mittl » a écrit : >I'm struggling with the electron density shown in the attachment. The

Re: [ccp4bb] unknown density

board on behalf of Jon >> Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> >> *Sent:* Monday, March 22, 2021 5:38:40 PM >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* Re: [ccp4bb] unknown density >> >> Definitely water pentamer, no doubt at all ;-

Re: [ccp4bb] unknown density

gt; *From:* CCP4 bulletin board on behalf of Jon > Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> > *Sent:* Monday, March 22, 2021 5:38:40 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] unknown density > > Definitely water pentamer, no doubt at all ;-0

Re: [ccp4bb] unknown density

Germany Phone: +49 (0)30 94793-284 From: CCP4 bulletin board on behalf of Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> Sent: Monday, March 22, 2021 5:38:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] unknown density Definitely water pe

Re: [ccp4bb] unknown density

<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] unknown density Hi Please look at the pic attached. found similar pentagon water network. On Mon, Mar 22, 2021 at 12:40 PM Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.

Re: [ccp4bb] unknown density

Definitely water pentamer, no doubt at all ;-0 Cheers, Jon.C. Sent from ProtonMail mobile Original Message On 22 Mar 2021, 14:16, Mark J. van Raaij wrote: > The ring looks too big to be imidazole or a nucleotide or a carbohydrate, so > it’s probably mainly water molecules. >

Re: [ccp4bb] unknown density

The ring looks too big to be imidazole or a nucleotide or a carbohydrate, so it’s probably mainly water molecules. Perhaps partially replaced by PEG to explain the density between them (i.e. water molecules in most copies of the protein and PEG in some other copies). I’ve seen horse-shoe shaped

Re: [ccp4bb] unknown density

Could be 5 water molecules. Pentagons of water molecules are common in high resolution structures. Add 5 waters and see if the inter-water distances are appropriate for hydrogen bonding (2.5-3.2 A). From: CCP4 bulletin board on behalf of Sam Tang Date: Monday, March 22, 2021 at 9:00 AM To:

Re: [ccp4bb] Unknown density

There is no blue (2fo-fc) density at least at the current contour level in your difference density.  That probably indicates what you are seeing is noise rather than a real feature. I am also seeing more intense (above 7 sigma in some cases) positive difference density without actual density

Re: [ccp4bb] Unknown density

Oops. I meant to say that Ca2+ usually has seven coordinating atoms. Mg2+ usually has six. Sorry for the error. -Daniel On Wed, Mar 7, 2018 at 2:27 PM, Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> wrote: > Rajesh, > > Ca2+ usually is coordinated by five atoms, whereas Mg2+ usually is >

Re: [ccp4bb] Unknown density

I would not rely only on coordination numbers, since Ca2+ can be also hepta-coordinated. You can look at the high resolution structures of parvalbumin and nucleoside hydrolases. And, although not up to date, this site is also useful http://mespeus.bch.ed.ac.uk/tanna/ . The anomalous map

Re: [ccp4bb] Unknown density

Rajesh, Ca2+ usually is coordinated by five atoms, whereas Mg2+ usually is coordinated by six. I've seen that a lot in structures that I've determined. -Daniel On Wed, Mar 7, 2018 at 2:14 PM, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > You just calculate a anom

Re: [ccp4bb] Unknown density

You just calculate a anom map - it doesnt need you to dselect Ca or Mg or anything else.. Judge the peak heights by the signal you get over any S sites in the model. The relative signal you expect depends on your wavelength of course. Eleanor On 7 March 2018 at 19:09, Rajesh Kumar

Re: [ccp4bb] Unknown density

Hi Ivan, https://csgid.org/csgid/metal_sites/ suggest that Mg++ is the correct metal. Ca++ is not acceptable. I am going to validate it by calculating anomalous peak for Ca++ too. Thank you Rajesh On Wed, Mar 7, 2018 at 1:06 PM, Ivan Shabalin < iva...@iwonka.med.virginia.edu> wrote: > Hi,

Re: [ccp4bb] Unknown density

Hi, Rajesh, It does look like Ca to me. It has around 2.4 A distances to waters and quite many electrons (18), which correspond to rather wide and high density peak in the middle. Mg has distances at 2.07, and 10 electrons (should be a smaller peak). Na has 2.41 distances to waters, 10

Re: [ccp4bb] Unknown density

Hi Rajesh, It might be water molecules present at the symmetry axis, one more water molecule at the centre (exactly at the axis, with occupancy of 0.5). If you put three water molecule you probably may find the other three symmetry-mates water molecules in opposite sides. OR One water molecule

Re: [ccp4bb] Unknown density

Hi Rajesh, You may find this database is also useful while refining your model http://mespeus.bch.ed.ac.uk/MESPEUS_10/ and for calcium http://mespeus.bch.ed.ac.uk/MESPEUS_10/_5.jsp Abhik On Tue, Mar 6, 2018 at 10:59 PM, Patrick Loll wrote: > Calcium likes to form

Re: [ccp4bb] Unknown density

Calcium likes to form octahedral complexes with water (or other oxygen-containing) ligands. This looks like a classic example. After you model and refine this, you’ll want to check water-metal distances, to make sure they are appropriate for calcium. There is a nice literature on such things,

Re: [ccp4bb] Unknown density

You could try to put CA (as you have CA in your crystallisation condition) and waters for coordinating atoms. If after refinement distances are around 2.3-2.4 (if I remember correctly) and B values of atoms (CA and waters) are consistent, i.e. similar to each other then CA is good

Re: [ccp4bb] Unknown density

Hi Rajesh, Can you please let everyone know the buffer/reagents involved throughout the process. Also, how strong is the density? In other words, until what contour level you see it in the Fo-Fc map? Anyways, looking at the shape, it looks well coordinated - could be cacodylate? Or water, am

Re: [ccp4bb] Unknown density

Hi Hussain, Crystallization condition is 200 mM CaCl2 and 20% PEG 3350. I some what realized that it could be Ca++ with coordinated waters. But I really wanted to have second opinion from our group. Thank you every one. -Rajesh On Tue, Mar 6, 2018 at 5:37 PM, Hussain Gps

Re: [ccp4bb] Unknown density

Mg2+(H20)6 ? > On 6 Mar 2018, at 22:19, Rajesh Kumar wrote: > > Dear All, > > Have you had experience with this kind of density? I am wandering what this > could be? > > Thank you very much for the help. > > -Rajesh > > > >

Re: [ccp4bb] Unknown density

It looks like 6 coordinated metal atom with coordinated (possibly) with waters. The simplest case could be NA. You could use anomalous difference map to see if there is any anomalous signal there. Regards Garib On 6 Mar 2018, at 22:19, Rajesh Kumar wrote: > Dear All,

Re: [ccp4bb] Unknown density

Dear Pavel, Is this density located on a symmetry axis? There is quite often a lot of noise around these regions - and it may not, in fact, be possible to model this satisfactorily. Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and

Re: [ccp4bb] Unknown density

Dear Pavel, you should also always consider your cryoprotectant molecules, so let's say if you used PEG for cryoprotection, there's a very high probability you may see it in your structure. It's very hard to say from the snapshots, but for the patch of density depicted in fig.2 I would try PEG

Re: [ccp4bb] Unknown density

Dear all, Thank you very much for help! The problem was solved very easy (thanks Dominik A. Herbs). I just used another program for refinement (Refmac5 instead Phenix.refine) and this noisy density almost disappeared. http://www.4sync.com/photo/--e2gHrG/Density-Refmac5.html Thanks a lot for

Re: [ccp4bb] unknown density

Hi Cedric, I presume you collected the datset at a synchrtron source. It could be free radical generated due to X-ray radiation has modified the glutamate residues. I have seen this happening for Ser residues. Cheers, Shiva On Wed, May 18, 2011 at 9:08 AM, cedric bauvois cbauv...@gmail.com

Re: [ccp4bb] unknown density

But that's a lysine, so maybe a PTM ? Acetylated perhaps ? Jürgen On May 18, 2011, at 1:56 PM, Shiva Bhowmik wrote: Hi Cedric, I presume you collected the datset at a synchrtron source. It could be free radical generated due to X-ray radiation has modified the glutamate residues. I have seen

Re: [ccp4bb] unknown density

I take the lysine back, just realized wrong color coding it's an oxygen and not a nitrogen closer to the extra density :-) Jürgen On May 18, 2011, at 2:03 PM, Bosch, Juergen wrote: But that's a lysine, so maybe a PTM ? Acetylated perhaps ? Jürgen On May 18, 2011, at 1:56 PM, Shiva Bhowmik

Re: [ccp4bb] unknown density

*To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] unknown density I take the lysine back, just realized wrong color coding it's an oxygen and not a nitrogen closer to the extra density :-) Jürgen On May 18, 2011, at 2:03 PM, Bosch, Juergen wrote: But that's a lysine, so maybe a PTM

Re: [ccp4bb] unknown density

Hi, I did a little bit of modeling in your density (starting from a nicotinamide ring, the positioned nicotinamide is enclosed). The middle part looks suspiciously like a 6 membered ring. Could it be a molecule in a half-chair conformation? There is only the blob that is perpendicular to the

Re: [ccp4bb] unknown density

...@formulatrix.com] Sent: Friday, October 01, 2010 9:18 AM To: Priscila Oliveira de Giuseppe Subject: Re: [ccp4bb] unknown density Hi Priscilla, I don't think a lot of people will take the trouble to find out for themselves which format your map files have... Its better to send screen shots, better still to put

Re: [ccp4bb] unknown density

and not PEG. Good luck! Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Priscila Oliveira de Giuseppe Sent: Friday, October 01, 2010 4:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] unknown density Hi Flip, Following your suggestion

Re: [ccp4bb] unknown density

+0200 From: herman.schreu...@sanofi-aventis.com Subject: Re: [ccp4bb] unknown density To: CCP4BB@JISCMAIL.AC.UK Hi Priscalla and Flip, I did not bother to find out what format the maps had, I just loaded them in coot with no problems. I fitted a cyclohexane ring with three atoms attached

Re: [ccp4bb] unknown density

as it appears to bear near the guanidine group of an arginine, I would suggest it is a partially occupied and disordered sulphate and/or phosphate. whether this is practically modellable is another matter, a sulphate at occ. 0.5 is an option, or putting a water with a remark in the pdb

Re: [ccp4bb] unknown density

Hi Katja, What I personally do in such a situation is to start to fill the density by water oxygen atoms, refine a bit (the position plus the isotropic temperature factors) and then compute a new map. Usually it has cleared up somewhat, thus allowing you to find out what it really is. This is

Re: [ccp4bb] unknown density

On Wed, 2010-02-03 at 18:26 +0100, Mark J. van Raaij wrote: as it appears to bear near the guanidine group of an arginine, I would suggest it is a partially occupied and disordered sulphate and/or phosphate. If it's a sulphate, a look at the anomalous map should show something. --

Re: [ccp4bb] unknown density

General remark – if I may Putting nothing in: no significant effect on model and life in general Putting ‘something’ potentially wrong and misleading in: could be detrimental to your career BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Katja Schleider Sent:

Re: [ccp4bb] unknown density

I agree with many others: this is quite possibly sulfate or phosphate. If collected at 1.54A the anomalous map should help identify the presence of sulfur. Sulfate or phosphate may be present at lower than full occupancy. I would refine everything else you reasonably know in the model

Re: [ccp4bb] unknown density

Mark J. van Raaij wrote: as it appears to bear near the guanidine group of an arginine, I would suggest it is a partially occupied and disordered sulphate and/or phosphate. whether this is practically modellable is another matter, a sulphate at occ. 0.5 is an option, or putting a water with a

Re: [ccp4bb] unknown density

I think there is at least one more option here (relevant at least in some rare cases): Identifying what that something is likely to be can be significant and may advance your career Of course it is important to present supporting or otherwise evidence for the interpretation. As already discussed,

Re: [ccp4bb] Unknown density

How about a 3-fold disordered metal ion? Mark On 19 Aug 2009, at 17:07, Sampath Natarajan wrote: Dear All, Currently I'm modeling one structure with 2.6A data. I could find an unknown density which I located in the interface between the three similar subunits. This density shows very

Re: [ccp4bb] Unknown density

The density looks an awful lot like a polyatomic anion (sulfate, phosphate, etc.). It's hard to tell from the fixed images, but it appears to be tetrahedral. Is there any chance a polyatomic anion could be in the crystallization solution? Perhaps from the protein stock solution? Sampath

Re: [ccp4bb] unknown density

Dear Bert, Your density reminded me a little bit of the paper by Pearson et al. Biochemistry 39:8575-8584(2000) which describes the water structure in the catalytic center of urease. I just went back to it and it looks like Figure 3 in that paper may hint some similarities to your case, in that

Re: [ccp4bb] unknown density

Theoretically, citric acid can decompose into beta-ketoglutaric acid, and the latter may decarboxylate into malonic acid... Not sure if this happens in aqueous solutions, but if your citrate had malonate contamination and your enzyme prefers malonate to anything else - that's where it may have

Re: [ccp4bb] unknown density for a small molecule

Dear Mengxia, the lower part could well be a sulfate ion. For the upper part, it is difficult to guess from a static picture. Unfortunately, at the resolution you have there are no programs which can build an unknown small molecule from scratch according to the density. You have to guess, fit it

Re: [ccp4bb] unknown density for a small molecule

Hi, It could be all sorts of things, but the one that for some reason is stuck in my mind is isopentenyl phosphate (phosphate, not pyrophosphate!). Of course w/o seeing the density in 3D this is just a guess. Artem Dear All, When I was refining my structure, I found some unmodeled blobs,

Re: [ccp4bb] unknown density for a small molecule

Hi, If you could send in stereo mode of the density you want to get suggestion, it will be convenient for the well trained eyes. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Tue, Feb 10, 2009 at 3:16 PM, ar...@xtals.org wrote: Hi,

Re: [ccp4bb] unknown density for a small molecule

Hi Mengxiao, The density sure reminds me of a nucleotide. Note the pi-pi stacking of the planar part between Tyr and Phe, and in the third stereo picture you attached, projections at what could be the 2 and 6 positions remind me of Guanine... plus there are Arg, Lys, etc. pointing toward

Re: [ccp4bb] unknown density for a small molecule

It could be purine or pyrimidine ring stacked between the Phe an Tyr. check pdb 3etr or 3eub of xanthine oxidase binding purine substrates between two Phe at the active site. Hongnan Cao UCR Date: Tue, 10 Feb 2009 00:23:54 -0500From: lvmengx...@gmail.comsubject: [ccp4bb] unknown density

Re: [ccp4bb] Unknown density

Remember that since it is on a special position (2-fold?), you may not be looking at a single object, but an overlay from two or more positions. The anomalous map is very useful; the mystery molecule must have an anomalous scatterer. It would be even more helpful if you had mentioned the

Re: [ccp4bb] unknown density in structure

-N-C(=O)-CH3 And so forth. Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Wu, Mousheng Sent: Thursday, July 26, 2007 6:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] unknown density in structure There are four molecules

Re: [ccp4bb] unknown density in structure

There are four molecules in the asymmetric unit. And this density is present in every molecules. -Original Message- From: ANA MARIA MISIC [mailto:[EMAIL PROTECTED] Sent: Thursday, July 26, 2007 5:24 PM To: Wu, Mousheng Subject: Re: [ccp4bb] unknown density in structure Hi Mousheng