Depositing NMR Structures with ADIT-NMR
Users can now deposit NMR structure and experimental data using
one tool: ADIT-NMR. Available from
ADIT-NMR can be used to precheck, validate, and deposit NMR structures.
Coordinates and constraint data will be processed and released
by the RCSB PDB, while other NMR spectral data (such as
chemical shifts, coupling constants, and relaxation parameters,
etc.) will be processed and archived by BMRB.
All new NMR depositions at RCSB PDB will be submitted using
ADIT-NMR. The assignment of PDB/BMRB IDs and the movement of
data files between sites is fully automated. More than 100
joint depositions have already been processed through this new
system. Any unfinished NMR deposition sessions that were
started using ADIT before May 16, 2007 will continue to be
available at that site.
Other tools for NMR depositions include:
minimizes errors and saves time during the deposition process
since fewer data items have to be manually entered.
The program extracts key details from the output files
produced by many X-ray crystallographic and NMR applications
for use in the deposition process. The program merges these
data into macromolecular Crystallographic Information File
(mmCIF) data files that can be used with ADIT-NMR to perform
validation and to add any additional information for PDB
pdb_extract can be used via web interface or downloadable
The Validation Server lets users check the format consistency
of coordinates (PRECHECK) and to create validation reports
about a structure before deposition (VALIDATION). These checks
can be done independently by the user. The Validation Server
can be used at the RCSB PDB (http://deposit.pdb.org/validate/) and
NMR structures may also be deposited using ADIT at PDBj and
AutoDep at MSD-EBI.
PDB Focus: First Time ADIT Depositors...
There are a few steps a depositor can take to make the process
of depositing a structure to the PDB quick, easy, and accurate!
This is an iterative process. If you encounter problems at a
particular step, please make the correction(s) and go through
the steps again.
1. Use the pdb_extract Program Suite to extract information
needed for deposition from output files produced by many
structure determination applications.
2. Check your structure with the Validation Server to ensure
that the data being deposited are accurate and reflect what
you intend to submit.
3. Compare your sequence with sequence database references.
Any necessary corrections can then be made to your sequence
and coordinates (Try BLAST at www.ebi.ac.uk/blast2 or
4. Use Ligand Depot to find the proper codes for existing
ligands, to link to other entries with a particular ligand,
and to search for substructures. If a ligand related to a
deposition is not in Ligand Depot, please email the chemical
diagram, name, and formula to email@example.com.
5. Deposit your structure using ADIT, using its editor to add
any missing information to the deposition.
For a detailed packet of information about first-time
deposition, including reprints about validation and Ligand
Depot, please send your postal address to
with the subject line "first time depositor packet".
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In the first half of 2007, 4535 structures were deposited to
the PDB archive.
The entries were processed by the wwPDB. Of the structures
deposited, 63.8% were deposited with a release status of "hold
until publication"; 17.9% were released as soon as annotation
of the entry was complete; and 18.3% were held until a
particular date. 83.7% of these entries were determined by
X-ray crystallographic methods; 16.1% were determined by NMR
methods. 84.1% of these structures were deposited with
experimental data. 93.7% of the crystal structures were
deposited with structure factors; 34.7% of NMR structures were
deposited with restraints.