Ah yes, polymer connectivity depends on the order of appearance not the numbering. On top of that, the connectivity is implicit. There are structures where some chains are numbered in reverse order, especially in double helices. How convenient is it that each base pair has residues of the same number 😉 This is a proper code breaker for many programs and indeed some of our code has this issue as well (we discovered this very recently and are fixing this).
What is even worse is that residues that are sequentially numbered are not necessarily connected. You can have residues 100 , 100A, 100B, 100C, 101 (yes, with insertion codes) and residues 100A, 100B and 100C were not modelled (or were deleted) because they did not have proper density. Many programs will gladly connect residue 100 to 101 and rip the structure to shreds when you do some sort of refinement. Well, at least in the olden days. When you interpret a structure model, you really have to check whether a possible peptide bond has a sensible length. Of course, you get away with not checking 99.99% of the time. But the PDB is pretty big nowadays... Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <[email protected]> On Behalf Of Dale > Tronrud > Sent: Friday, December 4, 2020 19:16 > To: [email protected] > Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the > PDB -- N-glycans are now separate chains if more than one residue > > Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is exactly > the > problem. "chain names" ( or "entity identifiers" if I recall the mmCIF > terminology correctly) are simply database "indexes". > The values of indices are meaningless in themselves, they are just unique > values that can be used to unambiguously identify a record. In principle, you > could just assign random ISO characters (I don't think mmCIF allows unicode) > and the mmCIF would be considered identical. > > You are trying to force meaning to the characters with an index, and that > puts multiple types of information in a single field. As Robbie said already > exists, if you want to encode connectivity into the data base you have to add > records that define that connectivity. That places the connectivity > information explicitly in the data models and allows standard data base tools > to track and validate. > > The idioms of the PDB cause problems that lead people to these mistakes. > The PDB assigns the indices "1", "2", and "3" to residues in a chain. A > person > could be misled into thinking that "2" comes between "1" and "3" in the > sequence. This is not necessarily true at all. To learn the sequence you > have > to go to the mmCIF records that define the connectivity between residues. > It is entirely possible that "3" comes before "1" because these indexes don't > contain any information, other than being unique within the chain. > > Dale Tronrud > > On 12/4/2020 9:46 AM, Tristan Croll wrote: > > This suggestion violates a basic principle of data base theory. A > > single data item cannot encode two pieces of information. > > > > I'm sorry if I was unclear, but I don't believe I was suggesting > > anything of the sort. Hopefully this example should make it more clear > > - I'm just suggesting a slight variation on the existing system, no more: > > > > If we start with model containing 3 protein chains A-C, with chain A > > containing amino acid residues 1-200, and 3 N-linked glycans with > > residues numbered, say, 1000-1005, 1020-1026 and 1040-1043 (a fairly > > common approach I've seen taken to the problem in the past, and one > > I've taken myself), then if I understand correctly after remediation > > we'll have a model with protein chains A-C and glycan chains D-F. The > > problem is, unless and until all the available visualisation software > > updates to automatically associate chains D-F to chain A based on > > linkage, the user just has to remember that chains D-F are actually the > chain A glycans. > > This is a simple case, but things quickly become far more messy when > > you have multiple glycosylated species each with multiple glycans per > chain. > > If, instead, the new chain assignments were something like "A, B, C, > > Ag1, Ag2, Ag3", then we have something that is far more immediately > > accessible to the user. > > > > ---------------------------------------------------------------------- > > -- > > *From:* Dale Tronrud <[email protected]> > > *Sent:* 04 December 2020 17:01 > > *To:* Tristan Croll <[email protected]>; [email protected] > > <[email protected]> > > *Subject:* Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at > > the PDB -- N-glycans are now separate chains if more than one residue > > > >    This suggestion violates a basic principle of data base theory. > > A single data item cannot encode two pieces of information. The whole > > structure of CIF falls apart if this is done. > > > >    Does the new PDB convention contain a CIF record of the link that > > bridges between the protein chain and the, now separated, glycan chain? > >  If not, I think this is the principle failing of their new scheme. > > > > Dale Tronrud > > > > On 12/4/2020 12:06 AM, Tristan Croll wrote: > >> To go one step further: in large, heavily glycosylated multi-chain > >> complexes the assignment of a random new chain ID to each glycan will > >> lead to headaches for people building visualisations using existing > >> viewers, because it loses the easy name-based association of glycan > >> to parent protein chain. A suggestion: why not take full > > advantage of the mmCIF capability for multi-character chain IDs, and > > name them by appending characters to the parent chain ID? Using chain > > A as an example, perhaps the glycans could become Ag1, Ag2, etc.? > >> > >>> On 4 Dec 2020, at 07:48, Luca Jovine <[email protected]> wrote: > >>> > >>> CC: pdb-l > >>> > >>> Dear Zhijie and Robbie, > >>> > >>> I agree with both of you that the new carbohydrate chain assignment > convention that has been recently adopted by PDB introduces confusion, > not just for PDB-REDO but also - and especially - for end users. > >>> > >>> Could we kindly ask PDB to improve consistency by either assigning a > >>> separate chain to all covalently attached carbohydrates (regardless > >>> of whether one or more residues have been traced), or reverting to > >>> the old system (where N-/O-glycans inherited the same chain ID of > >>> the protein to which they are attached)? The current > > hybrid solution hardly seems optimal... > >>> > >>> Best regards, > >>> > >>> Luca > >>> > >>>> On 3 Dec 2020, at 20:17, Robbie Joosten > <[email protected]> wrote: > >>>> > >>>> Dear Zhijie, > >>>> > >>>> In generally I like the treatment of carbohydrates now as branched > polymers. I didn't realise there was an exception. It makes sense for unlinked > carbohydrate ligands, but not for N- or O-glycosylation sites as these might > change during model building or, in my case, carbohydrate rebuilding in > PDB-REDO powered by Coot. > > Thanks for pointing this out. > >>>> > >>>> Cheers, > >>>> Robbie > >>>> > >>>>> -----Original Message----- > >>>>> From: CCP4 bulletin board <[email protected]> On Behalf Of > >>>>> Zhijie Li > >>>>> Sent: Thursday, December 3, 2020 19:52 > >>>>> To: [email protected] > >>>>> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data > >>>>> at the PDB -- N-glycans are now separate chains if more than one > >>>>> residue > >>>>> > >>>>> Hi all, > >>>>> > >>>>> I was confused when I saw mysterious new glycan chains emerging > >>>>> during PDB deposition and spent quite some time trying to find out > >>>>> what was wrong with my coordinates. Then it occurred to me that a > >>>>> lot of recent structures also had tens of N-glycan chains. > >>>>> Finally I realized that this phenomenon is a consequence of this PDB > policy announced here in July. > >>>>> > >>>>> > >>>>> For future depositors who might also get puzzled, let's put it in > >>>>> a short > >>>>> sentence: O- and N-glycans are now separate chains if it they > >>>>> contain more than one residue; single residues remain with the > protein chain. > >>>>> > >>>>> > >>>>> > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2F > >>>>> www.wwpdb.org%2Fdocumentation%2Fcarbohydrate- > remediation&data= > >>>>> > 04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47 > %7 > >>>>> > Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684263065% > 7CU > >>>>> > nknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI > 6I > >>>>> > k1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mBrkCJECFpZyCih4kOCcCv > LT1Gz > >>>>> QHxD5GD7bZDI9s1s%3D&reserved=0 > > > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w > > .wwpdb.org%2Fdocumentation%2Fcarbohydrate- > remediation&data=04%7C01 > > > %7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7e > ef1cf > > > 4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684263065%7CUnknow > n%7CTWFpbG > > > Zsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6 > Mn0% > > > 3D%7C1000&sdata=mBrkCJECFpZyCih4kOCcCvLT1GzQHxD5GD7bZDI9s1 > s%3D& > > ;reserved=0> > >>>>> > >>>>> "Oligosaccharide molecules are classified as a new entity type, > >>>>> branched, assigned a unique chain ID (_atom_site.auth_asym_id) and > >>>>> a new mmCIF category introduced to define the type of branching > >>>>> (_pdbx_entity_branch.type) . " > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> I found the differential treatment of single-residue glycans and > >>>>> multi-residue glycans not only bit lack of aesthetics but also > >>>>> misleading. When a structure contains both NAG-NAG... and single > >>>>> NAG on N-glycosylation sites, it might be because of lack of > >>>>> density for building more residues, or because that some of the > >>>>> glycosylation sites are now indeed single NAGs (endoH etc.) while > >>>>> some others are not cleaved due to accessibility issues. > >>>>> Leaving NAGs on the protein chain while assigning NAG-NAG... to a > new chain, feels like suggesting something about their true oligomeric state. > >>>>> > >>>>> > >>>>> For example, for cryoEM structures, when one only builds a single > >>>>> NAG at a site does not necessarily mean that the protein was > >>>>> treated by endoH. In fact all sites are extended to at least > >>>>> tri-Man in most cases. Then why keeping some sites associated with > >>>>> the protein chain while others kicked out? > >>>>> > >>>>> Zhijie > >>>>> > >>>>> > >>>>> > >>>>> ________________________________ > >>>>> > >>>>> From: CCP4 bulletin board <[email protected]> on behalf of > >>>>> John Berrisford <[email protected]> > >>>>> Sent: Thursday, July 9, 2020 4:39 AM > >>>>> To: [email protected] <[email protected]> > >>>>> Subject: [ccp4bb] Coming July 29: Improved Carbohydrate Data at > >>>>> the PDB > >>>>> > >>>>> > >>>>> Dear CCP4BB > >>>>> > >>>>> PDB data will shortly incorporate a new data representation for > >>>>> carbohydrates in PDB entries and reference data that improves the > >>>>> Findability and Interoperability of these molecules in > >>>>> macromolecular structures. In order to remediate and improve the > >>>>> representation of carbohydrates across the archive, the wwPDB has: > >>>>> > >>>>> *standardized Chemical Component Dictionary nomenclature > following > >>>>> IUPAC-IUBMB recommendations *provided uniform representation > for > >>>>> oligosaccharides *adopted Glycoscience-community commonly used > >>>>> linear descriptors using community tools *annotated glycosylation > >>>>> sites in PDB structures > >>>>> > >>>>> Starting July 29, 2020, users will be able to access the improved > >>>>> data via FTP or wwPDB partner websites. Detailed information about > >>>>> this project is available at the wwPDB website > >>>>> > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2 > >>>>> Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate- > remediation&data > >>>>> > =04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b4 > 7% > >>>>> > 7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018 > %7C > >>>>> > Unknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBT > iI6 > >>>>> > Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6begIrz7OgNq8CecxMhAh > m3n%2 > >>>>> F4WPAMM%2F4dg9uwmlrcs%3D&reserved=0 > > > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w > > .wwpdb.org%2Fdocumentation%2Fcarbohydrate- > remediation&data=04%7C01 > > > %7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7e > ef1cf > > > 4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknow > n%7CTWFpbG > > > Zsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6 > Mn0% > > > 3D%7C1000&sdata=6begIrz7OgNq8CecxMhAhm3n%2F4WPAMM%2F4d > g9uwmlrcs%3D > > &reserved=0>> > > ; lists > >>>>> of impacted entries and chemical components will be published on > >>>>> this page after data release. > >>>>> > >>>>> The wwPDB has created a new ‘branched’ entity representation for > >>>>> polysaccharides, describing all the individual monosaccharide > >>>>> components of these in the PDB entry. As part of this process, we > >>>>> have standardized atom nomenclature of >1,000 monosaccharides in > >>>>> the Chemical Component Dictionary (CCD) and applied a branched > >>>>> entity representation to oligosaccharides for >8000 PDB entries. > >>>>> To guarantee unambiguous chemical description of oligosaccharides > >>>>> in the affected PDB entries, an explicit description of covalent > >>>>> linkage information between their monosaccharide units is > >>>>> included. In addition, wwPDB validation reports provide consistent > >>>>> representation for these oligosaccharides and include 2D > representations based on the Symbol Nomenclature for Glycans (SNFG). > >>>>> > >>>>> To support the remediation of carbohydrate representation, > >>>>> software tools providing linear descriptors were developed in > >>>>> collaboration with the glycoscience community to enable easy > >>>>> translation of PDB data to other representations commonly used by > >>>>> glycobiologists. These include Condense IUPAC from GMML > >>>>> > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2 > >>>>> Fgithub.com%2FGLYCAM- > Web%2Fgmml&data=04%7C01%7Cluca.jovine%40K > >>>>> > I.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1d > d > >>>>> > a043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZs > b3d8eyJW > >>>>> > IjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C > 1 > >>>>> > 000&sdata=eA9rmh0D7QoyPzvwUBC%2BtIgZxdnQ72QWTx74CWQwpW > M%3D& > >>>>> ;reserved=0 > > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit > > hub.com%2FGLYCAM- > Web%2Fgmml&data=04%7C01%7Cluca.jovine%40KI.SE%7C1 > > > d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05 > d%7C0 > > > %7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiM > C4wLjAwMDAi > > > LCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=e > A9rmh > > > 0D7QoyPzvwUBC%2BtIgZxdnQ72QWTx74CWQwpWM%3D&reserved=0 > >> > > at University > >>>>> of Georgia, WURCS > >>>>> > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2 > >>>>> > Fgitlab.com%2Fglyconavi%2Fpdb2glycan&data=04%7C01%7Cluca.jovin > >>>>> > e%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32b > e3 > >>>>> > da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWF > pbGZsb3d > >>>>> > 8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0% > 3 > >>>>> > D%7C1000&sdata=TTLXk1QkfdzpSEozxxPuHf58f0EGYjnktH8uNOfoDe0% > 3D& > >>>>> amp;reserved=0 > > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit > > > lab.com%2Fglyconavi%2Fpdb2glycan&data=04%7C01%7Cluca.jovine%4 > 0KI.S > > > E%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda > 043c05 > > > d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJ > WIjoiMC4wLjA > > > wMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&s > data=T > > TLXk1QkfdzpSEozxxPuHf58f0EGYjnktH8uNOfoDe0%3D&reserved=0>> > > from > >>>>> PDB2Glycan at The Noguchi Institute, Japan, and LINUCS > >>>>> > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2F > >>>>> > www.glycosciences.de%2Ftools%2Fpdb2linucs%2F&data=04%7C01%7C > lu > >>>>> > ca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4 > >>>>> > b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown > %7CTWF > >>>>> > pbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXV > >>>>> > CI6Mn0%3D%7C1000&sdata=dXclDI7KsaKEajEuBxnbxY%2BjshExxyESN2 > RKD > >>>>> gJdr%2Fo%3D&reserved=0 > > > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww > . > > > glycosciences.de%2Ftools%2Fpdb2linucs%2F&data=04%7C01%7Cluca.j > ovin > > > e%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32b > e3da1d > > > da043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZ > sb3d8eyJWIjo > > > iMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C10 > 00& > > > ;sdata=dXclDI7KsaKEajEuBxnbxY%2BjshExxyESN2RKDgJdr%2Fo%3D&res > erved > > =0>> > > from pdb-care at > >>>>> Germany. > >>>>> > >>>>> Furthermore, to ensure continued Findability of 118 common > >>>>> oligosaccharides (e.g., sucrose, Lewis Y antigen), we have > >>>>> expanded the Biologically Interesting molecule Reference > >>>>> Dictionary (BIRD > >>>>> > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2 > >>>>> > Fwww.wwpdb.org%2Fdata%2Fbird&data=04%7C01%7Cluca.jovine%40 > KI.S > >>>>> > E%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda > 04 > >>>>> > 3c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d > 8eyJWIjo > >>>>> > iMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C10 > 00 > >>>>> > &sdata=feM%2F6RPoFqQwdIABus%2BD60JSTSbdi2UzsV62IRKX%2Fvg% > 3D&am > >>>>> p;reserved=0 > > > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w > > > .wwpdb.org%2Fdata%2Fbird&data=04%7C01%7Cluca.jovine%40KI.SE% > 7C1d79 > > > 0a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d% > 7C0%7C > > > 1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4w > LjAwMDAiLCJ > > > QIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=feM > %2F6RP > > oFqQwdIABus%2BD60JSTSbdi2UzsV62IRKX%2Fvg%3D&reserved=0>> > > ) that contains the covalent linkage > >>>>> information and common synonyms for such molecules. > >>>>> > >>>>> wwPDB has also used this opportunity to improve the organization > >>>>> of chemical synonyms in the CCD by introducing a new > >>>>> _pdbx_chem_comp_synonyms data category. This will enable more > >>>>> comprehensive capture of alternative names for small molecules in > the PDB. > >>>>> To minimize disruption to users, the legacy data item, > >>>>> _chem_comp.pdbx_synonyms, will be retained for a transition period > >>>>> through 2021. > >>>>> > >>>>> The carbohydrate remediation project is a wwPDB collaborative > >>>>> project that is carried out principally by RCSB PDB > >>>>> > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2 > >>>>> > Fwww.rcsb.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a > 07 > >>>>> > 17ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0% > 7C > >>>>> > 1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4w > LjAwMDA > >>>>> > iLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2 > >>>>> > 8mQbs4C%2FKygkU5GY1mNYzfX6Y1a76onFlsFwcpsVZU%3D&reserved= > 0 > > > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w > > > .rcsb.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717c > e4217 > > > c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C6 > 3742619 > > > 9684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQI > joiV2luMzI > > > iLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=28mQbs4C%2FKy > gkU5GY1m > > NYzfX6Y1a76onFlsFwcpsVZU%3D&reserved=0>> > > at Rutgers, > >>>>> The State University of New Jersey and is funded by NIGMS grant > >>>>> U01 > >>>>> CA221216 in collaboration with Complex Carbohydrate Research > >>>>> Center > >>>>> > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2 > >>>>> > Fwww.ccrc.uga.edu%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d > 79 > >>>>> > 0a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d% > 7C > >>>>> > 0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoi > MC4wLjA > >>>>> > wMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&s > da > >>>>> > ta=gkU8DWkdVXFE%2BCjcV2mEbU6I%2FECM5Dlq2XCErqtQEKk%3D&r > eserved > >>>>> =0 > > > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w > > > .ccrc.uga.edu%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0 > 717ce > > > 4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1 > %7C6374 > > > 26199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAi > LCJQIjoiV2l > > > uMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gkU8DWkdV > XFE%2BCj > > cV2mEbU6I%2FECM5Dlq2XCErqtQEKk%3D&reserved=0>> > > at the University of Georgia. > >>>>> > >>>>> If you have any comments or queries regarding the changes to > >>>>> carbohydrate representation, please visit the wwPDB website > >>>>> > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2 > >>>>> Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate- > remediation&data > >>>>> > =04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b4 > 7% > >>>>> > 7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018 > %7C > >>>>> > Unknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBT > iI6 > >>>>> > Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6begIrz7OgNq8CecxMhAh > m3n%2 > >>>>> F4WPAMM%2F4dg9uwmlrcs%3D&reserved=0 > > > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w > > .wwpdb.org%2Fdocumentation%2Fcarbohydrate- > remediation&data=04%7C01 > > > %7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7e > ef1cf > > > 4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknow > n%7CTWFpbG > > > Zsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6 > Mn0% > > > 3D%7C1000&sdata=6begIrz7OgNq8CecxMhAhm3n%2F4WPAMM%2F4d > g9uwmlrcs%3D > > &reserved=0>> > > or > >>>>> contact us at [email protected] <mailto:deposit- > >>>>> [email protected]> . > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> Regards > >>>>> > >>>>> > >>>>> > >>>>> John > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> > >>>>> John Berrisford > >>>>> > >>>>> PDBe > >>>>> > >>>>> European Bioinformatics Institute (EMBL-EBI) > >>>>> > >>>>> European Molecular Biology Laboratory > >>>>> > >>>>> Wellcome Trust Genome Campus > >>>>> > >>>>> Hinxton > >>>>> > >>>>> Cambridge CB10 1SD UK > >>>>> > >>>>> Tel: +44 1223 492529 > >>>>> > >>>>> > >>>>> > >>>>> > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fw > >>>>> > ww.pdbe.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0 > 717 > >>>>> > ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7 > C1% > >>>>> > 7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjA > wMDAiL > >>>>> > CJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jt > Q > >>>>> > QunJvDpFvpPIo3b%2BgX0ETtF5TeAvPE07SMtoClQs%3D&reserved=0 > > > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww > . > > > pdbe.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717c > e4217c > > > 7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C63 > 7426199 > > > 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> > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftwit > > > ter.com%2FPDBeurope&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d7 > 90a071 > > > 7ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7 > C1%7C6 > > > 37426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwM > DAiLCJQIjoi > > > V2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mphXsd3 > vaMR3wl > > OQ7%2F7p%2FaI3MKG3LPCGSyfVNg%2FCwrg%3D&reserved=0 > > > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftwit > > > ter.com%2FPDBeurope&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d7 > 90a071 > > > 7ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7 > C1%7C6 > > > 37426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwM > DAiLCJQIjoi > > > V2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mphXsd3 > vaMR3wl > > OQ7%2F7p%2FaI3MKG3LPCGSyfVNg%2FCwrg%3D&reserved=0>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ________________________________ > >>>>> > >>>>> To unsubscribe from the 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