{"id":"6631067e-22ad-5a15-856c-a26a26433a1b","stable_key":"33bef151-bdc7-5892-aff6-0345ab149739:the-crystal-structure-carries-modelled-calcium","predicate":"binds","statement":"The deposited 1.36 A subtilisin NAT structure models four calcium ions across its two chains, and the 1.74 A native structure is a monomeric assembly of one 275-residue chain.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"context_dependent","is_public":true,"mechanism_event_id":"5eca02cc-0095-52c4-9fca-22787341dc69","mechanism_event_label":"The deposited 1.36 A subtilisin NAT structure models four calcium ions across its two chains, and the 1.74 A native structure is a monomeric assembly of one 275-residue chain.","subject":{"id":"6b03a125-209a-5060-8b35-ec9e0e54033c","slug":"nattokinase","display_name":"Nattokinase / subtilisin NAT","entity_type_key":"peptide"},"object":{"id":"e359bc15-e675-5d83-b0fe-1d70814e130b","slug":"calcium-ion","display_name":"Calcium ion","entity_type_key":"ion"},"evidence_count":1,"mechanism_event":{"id":"5eca02cc-0095-52c4-9fca-22787341dc69","stable_key":"33bef151-bdc7-5892-aff6-0345ab149739:the-crystal-structure-carries-modelled-calcium-event","event_type":"biochemical_relationship","label":"The deposited 1.36 A subtilisin NAT structure models four calcium ions across its two chains, and the 1.74 A native structure is a monomeric assembly of one 275-residue chain.","description":"X-ray crystallography","status":"provisional","compartment":null,"participants":[{"entity":{"id":"6b03a125-209a-5060-8b35-ec9e0e54033c","slug":"nattokinase","display_name":"Nattokinase / subtilisin NAT","entity_type_key":"peptide"},"role":"acting component","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"e359bc15-e675-5d83-b0fe-1d70814e130b","slug":"calcium-ion","display_name":"Calcium ion","entity_type_key":"ion"},"role":"component the finding is about","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""}]},"contexts":[{"dimension":"duration","value_text":"Not stated here","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"evidence_access","value_text":"RCSB Protein Data Bank entry metadata reviewed. No functional assay is attached to a structure record.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"Bacillus subtilis var. natto","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"exposure","value_text":"Not applicable","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"A deposited crystal structure is not a solution stoichiometry. Calcium occupancy here is what was modelled into density, and no functional calcium requirement is measured by these entries.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"organism","value_text":"Bacillus subtilis var. natto","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"The deposited 1.36 A subtilisin NAT structure models four calcium ions across its two chains, and the 1.74 A native structure is a monomeric assembly of one 275-residue chain.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[rcsb-3vyv] RCSB PDB entry 3VYV: crystal structure of subtilisin NAT at 1.36 A. (2013) https://www.rcsb.org/structure/3VYV Not indexed in PubMed.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"route","value_text":"In vitro","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue","value_text":"X-ray crystallography","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"d1ebf545-81b2-5cf3-874f-82f16633bda9","evidence_kind":"source_excerpt","locator":"Lines 92-92","start_line":92,"end_line":92,"excerpt":"The deposited 1.36 A subtilisin NAT structure models four calcium ions across its two chains, and the 1.74 A native structure is a monomeric assembly of one 275-residue chain.","model_system":"Bacillus subtilis var. natto","directness":"reported_statement","verification_status":"source_derived_draft","notes":"","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"41cb127c-1c23-53aa-b7d0-5ec7f6fa3c99","stable_key":"import-33bef151-bdc7-5892-aff6-0345ab149739","title":"Nattokinase: what the purified enzyme cleaves, what survives being eaten, and the gap between the two (2026-09-23)","document_type":"imported_text","citation_label":"Original AI-assisted curation built from a supplied entity-first document of 105 entities and 129 claims. Every reference in that document was resolved against live PubMed with its abstract read and its DOI cross-checked on 2026-09-23, and the EFSA novel-food opinion was retrieved and read in full. That check corrected two PMIDs that pointed at unrelated papers, two DOIs, and two papers recorded as carrying no erratum that do carry one; it also reversed three findings the supplied document had stated backwards. Two papers carry a published correction, recorded as such and not as a retraction. Three sources are not indexed in PubMed and are cited by what they have. Laboratory lineages are recorded, so the four papers from one group, the three from another and the two readings of a single applicant dossier cannot be counted as separate lines of support. Study-specific doses, units, populations and limitations retained; activity units are never converted between systems. Not publisher full text.","file_path":"","sha256":"34fc46e0e849d06bfa13cb099a79b50679dd6fd0de8a5a0575326afdde3259c1","revision_id":"efd063e6-e982-5f6e-a4b8-6f2ffe4185ce","review_status":"unverified_draft","notes":""}}],"relations":[],"conflicts":[],"corrections":[],"research":null}