About PDBMLplus, PDBMLadd, and mmjson-plus
We already finished providing PDBMLplus files written in the XML format. Instead, please use PDBj Mine RDB search or the mmjson-plus files written in json format.
Introduction
Before we provided PDBMLplus as the merged data of PDBML, XML-formatted PDB data, and PDBMLadd, which includes additional information for each PDB entry and is originally created by PDBj. Although we no longer provide it in XML format, we continue to provide the file mmjson-plus, which contains the contents equivalent to PDBMLadd in json format (see 2021 PDBj web server transition - PDBj news 2021/05/23). This information is also available in the relational database used by PDBj's search service, PDBj Mine, so that you can also refer to this information in this search.
Contens and Resources
The PDBMLadd and mmjson-plus include the following contents. The information resources also described below.
Category | Elements | Resources etc. | |
---|---|---|---|
citation_author_pdbmlplus | auth_validate, citation_id, name, ordinal, pdbid, update_id | ||
citation_pdbmlplus | auth_validate, id, journal_abbrev, journal_volume, page_first, page_last, pdbid, pdbx_database_id_DOI, pdbx_database_id_PubMed, title, update_id, year | ||
exptl_crystal_grow_comp_pdbmlplus | auth_validate, chemical_formula, common_name, conc, conc_unit, crystal_id, details, id, pdbid, sol_id, update_id | ||
exptl_crystal_grow_pdbmlplus | auth_validate, crystal_id, method, pH, pH_range_high, pH_range_low, pdbid, pdbx_details, temp, temp_unit, update_id | ||
exptl_crystal_pdbmlplus | auth_validate, density_Matthews, density_percent_sol, id, pdbid, update_id | ||
gene_ontology_pdbmlplus | auth_asym_id, auth_validate, entry_id, goid, name, namespace, pdbid, source, update_id | The infomation of Gene Ontology extracted from UniProt. The elements of pdbid, auth_asym_id, and goid are extracted from SIFTS, created by PDBe, and namespace and name are from Gene Ontology. | |
history_pdbmlplus | id, literature, pdbid | ||
link_asym_pdbmlplus | asym_id, entity_id, pdb_strand_id, pdbid | ||
link_entity_pdbmlplus | db_accession, db_name, entity_id, pdbid | ||
link_entry_pdbmlplus | db_accession, db_name, pdbid | ||
refine_ls_restr_pdbmlplus | auth_validate, dev_ideal, dev_ideal_target, pdbid, pdbx_refine_id, type, update_id, weight | ||
refine_ls_shell_pdbmlplus | R_factor_R_free, R_factor_R_work, R_factor_all, R_factor_obs, auth_validate, d_res_high, d_res_low, number_reflns_R_free, number_reflns_work, number_reflns_obs, pdbid, pdbx_refine_id, pdbx_total_number_of_bins_used, percent_reflns_R_free, update_id | ||
refine_pdbmlplus | B_iso_mean, auth_validate, entry_id, Is_R_factor_R_free, Is_R_factor_R_work, Is_R_factor_all Is_R_factor_obs, Is_d_res_high, Is_d_res_low, Is_number_reflns_R_free, Is_number_reflns_all, Is_number_reflns_obs, Is_percent_reflns_R_free, pdbid, pdbx_Is_sigma_F, pdbx_Is_sigma_I, pdbx_refine_id, update_id | ||
reflns_pdbmlplus | B_iso_Wilson_estimate, Rmerge_F_obs, auth_validate, d_resolution_high, d_resolution_low, number_all, number_obs, observed_criterion_sigma_F, observed_criterion_sigma_I, pdbid, pdbx_Rmerge_I_obs, pdbx_number_measured_all, pdbx_ordinal, pdbx_redundancy, percent_possible_obs, update_id | ||
reflns_shell_pdbmlplus | Rmerge_I_obs, auth_validate, d_res_high, d_res_low, meanI_over_sigI_obs, number_measured_obs, number_possible, number_unique_obs, pdbid, pdbx_ordinal, pdbx_redundancy, percent_possible_obs, update_id | ||
software_pdbmlplus | auth_validate, classification, name, pdbid, pdbx_ordinal, update_id, version | ||
struct_ref_pdbmlplus | auth_validate, biological_source, cellular_location, db_name, entity_id, id, pdbid, pdbx_db_accession, update_id | Extracted from UniProt. | |
struct_ref_seq_pdbmlplus | align_id, auth_validate, db_align_beg, db_aling_end, pdbid, pdbx_auth_seq_align_beg, pdbx_auth_seq_align_end, pdbx_db_accession, pdbx_strand_id, ref_id, seq_align_beg, seq_align_end, update_id | ||
struct_ref_src_pdbmlplus | auth_validate, id, organ_source, pdbid, ref_id, update_id | ||
struct_site_gen_pdbmlplus | auth_asym_id, auth_seq_id, auth_validate, beg_auth_seq_id, beg_label_comp_id, beg_label_seq_id, details, end_auth_seq_id, end_label_comp_id, end_label_seq_id, id, label_asym_id, label_comp_id, label_seq_id, pdbid, site_id, update_id | Extracted from UniProt/SwissProt, Prosite, Catalytic Site Atlas (CSA), and CATRES. | |
struct_site_pdbmlplus | auth_validate, details, id, info_subtype, info_type, pdbid, pdbx_num_residues, update_id | Extracted from UniProt/SwissProt, Prosite, and Catalytic Site Atlas (CSA). |
URL
The URL of the mmjson-plus file is:
https://data.pdbjpw1.pdbj.org/pdbjplus/data/pdb/mmjson-plus/[PDBID]-plus.json.gz
Example: PDBID 100d
https://data.pdbjpw1.pdbj.org/pdbjplus/data/pdb/mmjson-plus/100d-plus.json.gz