Preparation Method of Chemical Shift

This page describes the creation of the chemical shift file from the data of biological molecules to deposit to BMRB.
Assigned chemical shift data must be described in NMR-STAR form. (NMR-STAR format is based on the atomic nomenclature of IUPAC)

*Data conversion tools for depositing to BMRB*
1, NMR-STAR template Generator : creates template NMR-STAR 3.1 data tables from residue sequence string.
2, STARch file converter :converts data files in various formats to NMR-STAR 3.1.

This article describes detail of tool 1(NMR-STAR template Generator)

1. Prepare Amino acid residue sequence (1 letter code, FASTA-format)

complete sequence of biological molecules

e.g. HHHHHHAFGCRESWQAKCLPHNMVIXSDF

2. Interacting with the tool

Click to NMR-STAR template Generator.

In this case, select "Assigned chemical shifts" as Data type, "polypeptide" as Residue type.
When you click button, the following page appears.

1. Enter the residue sequence into the text box.

2. Select atoms to include
If you select "Atoms observed in routine NMR studies", a chemical shift template for 1H, 13C and 15N will be created.
If you select "All atoms", a chemical shift template for all atoms will be created.
If you select "Backbone atoms (CA, C, N, HA, H)", a chemical shift template for the main chain will be created.

3. Specify the atoms you want to exclude from the list.

4. Specify the residues you want to include into the list.
If you enter nothing, a chemical shift template for all will be created.

5. If you select "All residues except those selected in the table", a chemical shift template except checking will be created.

Check "Include default ambiguity codes". Finally, click button and save this template file in text format.

3. fill in a form

e.g. NMR-STAR template
Click the above Link and open in a text editor or Excel.

The paragraph of code in the NMR-STAR template includes a loop.
The loop is arranged so that ‘Tags’ (identifiers of data types) are stored on separate lines and each line corresponded directly to a vertical column of data below (see example).
Thus line 1 ‘_Atom_chem_shift.ID’ corresponds to column 1, line 2 ‘_Atom_chem_shift.Entity_assembly_ID’ corresponds to column 2, etc.

Please replace the ‘@’ mark with your experimental data.

e.g.

4. Tag details

• _Atom_chem_shift.Val :
  Assigned chemical shift value.
  Note: fill in the form with the ppm unit and significant digits. (e.g.)2.19 or 2.190


• _Atom_chem_shift.Val_err :
  Estimated or measured error in the assigned chemical shift value. You can specify Value_error to each nuclide using ADIT-NMR. Note: fill in the form with the ppm unit.


• _Atom_chem_shift.Ambiguity :
  Ambiguity codes are used to define chemical shifts that have not been assigned to specific atoms in the molecule studied. Ambiguity in chemical shifts may exist at several different levels, stereospecific ambiguity, intra and inter residue ambiguities, etc.
  
  Note: The Ambiguity code is entered automatically. Please confirm whether these value are correct or not.
  Note:Assign ambiguity codes: This program checks an assigned chemical shifts table for possible "non-unique" assignments.

Ambiguity Code

1	Unique (geminal atoms and geminal methyl groups with identical chemical shifts are assumed to be assigned to stereospecific atoms)
2	Ambiguity of geminal atoms or geminal methyl proton groups (e.g. Asp HB2 and HB3 protons, Leu CD1 and CD2 carbons, or Leu HD1 and HD2 methyl protons)
3	Aromatic atoms on opposite sides of symmetrical rings (e.g. Tyr HE1 and HE2 protons)
4	Intraresidue ambiguities (e.g. Lys HG and HD protons or Trp HZ2 and HZ3 protons)
5	Interresidue ambiguities (Lys 12 vs. Lys 27)
6	Intermolecular ambiguities (e.g. Asp 31 CA in monomer 1 and Asp 31 CA in monomer 2 of a asymmetrical homodimer, duplex DNA assignments, or other assignments that may apply to atoms in one or more molecule in the molecular assembly)
9	Ambiguous, specific ambiguity not defined

If Ambiguity code is “4”, “5”

For ambiguity codes of 4 or 5, various combinations of assigned chemical shifts may form sets where the chemical shift assignments are not specifically known, but it is known that the chemical shifts belong to one atom in the set. The ambiguous shifts need to be grouped into sets using identifying integers.

• _Ambiguous_atom_chem_shift.Ambiguous_shift_set_ID :
  An integer value that defines a set of chemical shifts that form a mutually ambiguous group.
  Please assign a single number to identify a group.
  Numerous groups can exist, but each group must have a unique Ambiguous_shift_set_ID (1,2,3…)


• _Ambiguous_atom_chem_shift.Atom_chem_shift_ID :
  This number should correspond to the row number (_Atom_chem_shift.ID) that the atoms forming an ambiguous group are located (see example; the atoms at row 150 and 171 constitute a group (group 1) of ambiguous shifts, atoms at row 234 and 257 constitute group 2).

If there are blanks in NMR-STAR template

Keep or delete the blanks, either is fine.

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