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5 Easy Steps to PDB Deposition with Onedep

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5 Easy Steps to PDB Deposition with Onedep 5 Easy Steps to PDB Deposition with OneDep After Deposition Check Sample Check 3 Validate! Deposit your Entries are annotated, 1 2 3 Prepare Data Prepare4 Data 5 validated, and returned Sequence Ligands Validate! structure to authors for review for Deposition • Processed files and official validation report Sequence should Are your ligands already in Generate coordinate file in The wwPDB provides a Deposition to the OneDep can be downloaded at our Chemical Component PDBx/mmCIF format standalone validation server system can be carried • Contain all residues communication page Dictionary (CCD)? • This can be output directly for checking your structure out at the wwPDB • Include expression tags Check at: from some refinement Visit validate.wwpdb.org deposition pages. and disordered residues programs Visit deposit.wwpdb.org Request entry release and • Ligand Expo • Both model and experi- (e.g., PHENIX, REFMAC) provide citation publication ligand-expo.rcsb.org mental data are validated • This ensures that the information using OneDep’s Check against reference • PDBeChem • Provides detailed reports Deposition is tailored to maximum metadata is communication panel. database with BLAST pdbe.org/chem (PDF and XML files) experimental type: captured from the file for • X-ray, Neutron, NMR, • Proteins [ • Chemie search pdbj.org/chemie-search deposition EM, or any combination Coordinate release follows UniProt BLAST Attempt to fix major ! of these instructions given at • Nucleic acids [ issues highlighted prior • You must upload the deposition NCBI BLAST Is the ligand present pdb_extract can be used to deposition to minimize in the CCD? to extract information. relevant coordinate and the requirement for experimental data files • REL - released immediately Visit pdb-extract.wwpdb.org replacement files. It will after processing Any mismatch Yes The 3-character and include mandatory ! reduce the time needed should correspond to code for your • Creates single PDBx/ information • HPUB - hold until to process your entry. mutation, variant or ligand should mmCIF file containing publication, up to 1 year extra meta data (e.g., A session ID is provided to expression tag in match that in the • HOLD - hold up to 1 year your sequence. dictionary author info, enable you to continue your data collection and deposition at a later date. If the structure is not No During deposition refinement stats) using A PDB ID will be provided published within 1 year, you Example of a UniProt you can provide a output log files upon completion of your have the option to either alignment with highlighted SMILES or upload • Converts SF files to PDBx/ deposition. release or withdraw the entry. mismatch a 2D chemical mmCIF format for diagram non-MTZ format files Query Example of a chemical diagram that should be 61 RWWANDGRTPGSR provided at deposition RWW NDGRTPGSR 79 RWWCNDGRTPGSR P00698 (UniProt Sequence) Depending on the depositor’s geographical location, the structure will be assigned for processing to one of the worldwide Protein Data Bank sites: RCSB PDB, PDBe, or PDBj. Online resources Deposition Checklist PDB_extract: pdb-extract.wwpdb.org Validation: validate.wwpdb.org Deposition: deposit.wwpdb.org EASY 4 q Check sample sequence Further Information Refer to UniProt STEPS Tutorials and FAQs for validation and deposition 5 can be found at: q4 Check ligands www.wwpdb.org/validation/validation-reports TO PDB Are these correctly assigned? wwpdb.org/deposition/tutorial DEPOSITION wwpdb.org/deposition/faq q4 Prepare data for deposition Generate PDBx/mmCIF-formatted data Contact Information files to provide the most complete information about your structure [email protected] [email protected] 4 Validate your data q Citation Information Use wwPDB’s standalone validation service Cite wwPDB: Nature Structural Biology 10, 980 (2003) doi: 10.1038/nsb1203-980 PDB ID 4 1d1i q Deposit your structure using Cite OneDep: OneDep System Structure 25, 536-545 (2017) doi: 10.1016/j.str.2017.01.004 When you are ready wwPDB Members PDB ID 5a1a wwPDB.org wwpdb.org.
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