Depositing NMR Structures with ADIT-NMR

Users can now deposit NMR structure and experimental data using one tool: ADIT-NMR. Available from batfish.bmrb.wisc.edu/bmrb-adit and nmradit.protein.osaka-u.ac.jp/bmrb-adit, 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:

• pdb_extract ¹ 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 deposition.
  
  pdb_extract can be used via web interface or downloadable workstation from pdb-extract.rcsb.org.
  
  
• 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 PDBj (http://pdbdep.protein.osaka-u.ac.jp/validate/) sites.
  
  NMR structures may also be deposited using ADIT at PDBj and AutoDep at MSD-EBI.

¹ Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. (2004) Acta Cryst. D60, pp. 1833-1839.

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 www.ncbi.nih.gov/BLAST).

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 deposit@deposit.rcsb.org.

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 info@rcsb.org with the subject line "first time depositor packet".

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Deposition Statistics

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.