Entry Database : PDB / ID : 7loy Structure visualization Downloads & linksTitle Dihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum Components4-hydroxy-tetrahydrodipicolinate synthase Details Keywords LYASE / TIM BarrelFunction / homology Function and homology informationFunction Domain/homology Component
(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol Similarity search - Function 4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel Similarity search - Domain/homologyBiological species Candidatus Liberibacter solanacearum (bacteria)Method X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution : 2.4 Å DetailsAuthors Gilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J. Funding support 1items Details Hide detailsOrganization Grant number Country Not funded
CitationJournal : To Be Published Title : Dihydrodipicolinate synthase with pyruvate from the plant pathogen, Candidatus Liberibacter solanacearumAuthors : Gilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J. History Deposition Feb 11, 2021 Deposition site : RCSB / Processing site : RCSBRevision 1.0 Mar 3, 2021 Provider : repository / Type : Initial releaseRevision 2.0 Mar 15, 2023 Group : Advisory / Atomic model ... Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary Category : atom_site / atom_sites ... atom_site / atom_sites / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range Item : _atom_sites.fract_transf_matrix[1][3] / _database_2.pdbx_DOI ... _atom_sites.fract_transf_matrix[1][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_special_symmetry.auth_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_low / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id Description : Ligand geometryDetails : We have fixed errors we discovered in the ligand bound into the active site.Provider : author / Type : Coordinate replacementRevision 2.1 Oct 25, 2023 Group : Data collection / Refinement descriptionCategory : chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_modelItem : _pdbx_initial_refinement_model.detailsRevision 2.2 Nov 29, 2023 Group : Data collection / Category : chem_comp_atom / chem_comp_bond / Item : _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Show all Show less