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About PDBMLplus, PDBMLadd, and mmjson-plus

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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.pdbjbk1.pdbj.org/pdbjplus/data/pdb/mmjson-plus/[PDBID]-plus.json.gz

Example: PDBID 100d

https://data.pdbjbk1.pdbj.org/pdbjplus/data/pdb/mmjson-plus/100d-plus.json.gz

Created: 2022-11-18

217705

PDB entries from 2024-03-27

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