data_2YX8 # _entry.id 2YX8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2YX8 RCSB RCSB027248 WWPDB D_1000027248 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id hso002001341.1 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2YX8 _pdbx_database_status.recvd_initial_deposition_date 2007-04-24 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kusano, S.' 1 'Kukimoto-Niino, M.' 2 'Shirouzu, M.' 3 'Shindo, T.' 4 'Yokoyama, S.' 5 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 6 # _citation.id primary _citation.title 'Crystal structure of the human receptor activity-modifying protein 1 extracellular domain.' _citation.journal_abbrev 'Protein Sci.' _citation.journal_volume 17 _citation.page_first 1907 _citation.page_last 1914 _citation.year 2008 _citation.journal_id_ASTM PRCIEI _citation.country US _citation.journal_id_ISSN 0961-8368 _citation.journal_id_CSD 0795 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18725456 _citation.pdbx_database_id_DOI 10.1110/ps.036012.108 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Kusano, S.' 1 primary 'Kukimoto-Niino, M.' 2 primary 'Akasaka, R.' 3 primary 'Toyama, M.' 4 primary 'Terada, T.' 5 primary 'Shirouzu, M.' 6 primary 'Shindo, T.' 7 primary 'Yokoyama, S.' 8 # _cell.entry_id 2YX8 _cell.length_a 43.097 _cell.length_b 43.097 _cell.length_c 82.992 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 2YX8 _symmetry.space_group_name_H-M 'P 42 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 93 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Receptor activity-modifying protein 1' 10781.900 1 ? ? 'Extracellular Domain' ? 2 water nat water 18.015 17 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'CRLR activity- modifying protein 1, Calcitonin-receptor-like receptor activity- modifying protein 1' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;GSFTSSGCQEANYGALLRELCLTQFQVD(MSE)EAVGETLWCDWGRTIRSYRELADCTWH(MSE)AEKLGCFWPNAEVDR FFLAVHGRYFRSCPISGRAVR ; _entity_poly.pdbx_seq_one_letter_code_can ;GSFTSSGCQEANYGALLRELCLTQFQVDMEAVGETLWCDWGRTIRSYRELADCTWHMAEKLGCFWPNAEVDRFFLAVHGR YFRSCPISGRAVR ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier hso002001341.1 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 SER n 1 3 PHE n 1 4 THR n 1 5 SER n 1 6 SER n 1 7 GLY n 1 8 CYS n 1 9 GLN n 1 10 GLU n 1 11 ALA n 1 12 ASN n 1 13 TYR n 1 14 GLY n 1 15 ALA n 1 16 LEU n 1 17 LEU n 1 18 ARG n 1 19 GLU n 1 20 LEU n 1 21 CYS n 1 22 LEU n 1 23 THR n 1 24 GLN n 1 25 PHE n 1 26 GLN n 1 27 VAL n 1 28 ASP n 1 29 MSE n 1 30 GLU n 1 31 ALA n 1 32 VAL n 1 33 GLY n 1 34 GLU n 1 35 THR n 1 36 LEU n 1 37 TRP n 1 38 CYS n 1 39 ASP n 1 40 TRP n 1 41 GLY n 1 42 ARG n 1 43 THR n 1 44 ILE n 1 45 ARG n 1 46 SER n 1 47 TYR n 1 48 ARG n 1 49 GLU n 1 50 LEU n 1 51 ALA n 1 52 ASP n 1 53 CYS n 1 54 THR n 1 55 TRP n 1 56 HIS n 1 57 MSE n 1 58 ALA n 1 59 GLU n 1 60 LYS n 1 61 LEU n 1 62 GLY n 1 63 CYS n 1 64 PHE n 1 65 TRP n 1 66 PRO n 1 67 ASN n 1 68 ALA n 1 69 GLU n 1 70 VAL n 1 71 ASP n 1 72 ARG n 1 73 PHE n 1 74 PHE n 1 75 LEU n 1 76 ALA n 1 77 VAL n 1 78 HIS n 1 79 GLY n 1 80 ARG n 1 81 TYR n 1 82 PHE n 1 83 ARG n 1 84 SER n 1 85 CYS n 1 86 PRO n 1 87 ILE n 1 88 SER n 1 89 GLY n 1 90 ARG n 1 91 ALA n 1 92 VAL n 1 93 ARG n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus Homo _entity_src_gen.pdbx_gene_src_gene RAMP1 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type PLASMID _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PE060926-03 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code RAMP1_HUMAN _struct_ref.pdbx_db_accession O60894 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;CQEANYGALLRELCLTQFQVDMEAVGETLWCDWGRTIRSYRELADCTWHMAEKLGCFWPNAEVDRFFLAVHGRYFRSCPI SGRAVR ; _struct_ref.pdbx_align_begin 27 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2YX8 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 8 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 93 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O60894 _struct_ref_seq.db_align_beg 27 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 112 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 27 _struct_ref_seq.pdbx_auth_seq_align_end 112 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 2YX8 GLY A 1 ? UNP O60894 ? ? 'EXPRESSION TAG' 20 1 1 2YX8 SER A 2 ? UNP O60894 ? ? 'EXPRESSION TAG' 21 2 1 2YX8 PHE A 3 ? UNP O60894 ? ? 'EXPRESSION TAG' 22 3 1 2YX8 THR A 4 ? UNP O60894 ? ? 'EXPRESSION TAG' 23 4 1 2YX8 SER A 5 ? UNP O60894 ? ? 'EXPRESSION TAG' 24 5 1 2YX8 SER A 6 ? UNP O60894 ? ? 'EXPRESSION TAG' 25 6 1 2YX8 GLY A 7 ? UNP O60894 ? ? 'EXPRESSION TAG' 26 7 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2YX8 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.88 _exptl_crystal.density_percent_sol 31.159447 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.4 _exptl_crystal_grow.pdbx_details '0.1M tri-Sodium Citrate Dihydrate, 0.15M di-Ammonium Citrate, 25% PEG3350, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'RIGAKU JUPITER 210' _diffrn_detector.pdbx_collection_date 2007-03-26 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si double crystal' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9789 1.0 2 0.9793 1.0 3 0.9640 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL26B2' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL26B2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9789, 0.9793, 0.9640' # _reflns.entry_id 2YX8 _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.4 _reflns.number_obs 3371 _reflns.number_all ? _reflns.percent_possible_obs 99.3 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.095 _reflns.pdbx_netI_over_sigmaI 21.26 _reflns.B_iso_Wilson_estimate 30.0 _reflns.pdbx_redundancy 15.15 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.4 _reflns_shell.d_res_low 2.49 _reflns_shell.percent_possible_all 93.2 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.33 _reflns_shell.meanI_over_sigI_obs 2.59 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2YX8 _refine.ls_number_reflns_obs 3350 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 1048459.05 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 24.56 _refine.ls_d_res_high 2.40 _refine.ls_percent_reflns_obs 99.1 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.221 _refine.ls_R_factor_R_free 0.281 _refine.ls_R_factor_R_free_error 0.016 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.9 _refine.ls_number_reflns_R_free 333 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 36.7 _refine.aniso_B[1][1] 3.49 _refine.aniso_B[2][2] 3.49 _refine.aniso_B[3][3] -6.98 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.461846 _refine.solvent_model_param_bsol 54.2507 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 2YX8 _refine_analyze.Luzzati_coordinate_error_obs 0.29 _refine_analyze.Luzzati_sigma_a_obs 0.30 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.36 _refine_analyze.Luzzati_sigma_a_free 0.40 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 667 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 17 _refine_hist.number_atoms_total 684 _refine_hist.d_res_high 2.40 _refine_hist.d_res_low 24.56 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.1 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 20.1 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.68 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.40 _refine_ls_shell.d_res_low 2.55 _refine_ls_shell.number_reflns_R_work 451 _refine_ls_shell.R_factor_R_work 0.271 _refine_ls_shell.percent_reflns_obs 93.0 _refine_ls_shell.R_factor_R_free 0.348 _refine_ls_shell.R_factor_R_free_error 0.049 _refine_ls_shell.percent_reflns_R_free 10.2 _refine_ls_shell.number_reflns_R_free 51 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 protein_rep.param protein.top 'X-RAY DIFFRACTION' 2 water_rep.param water.top 'X-RAY DIFFRACTION' # _struct.entry_id 2YX8 _struct.title 'Crystal structure of the extracellular domain of human RAMP1' _struct.pdbx_descriptor 'Receptor activity-modifying protein 1' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2YX8 _struct_keywords.pdbx_keywords 'PROTEIN TRANSPORT' _struct_keywords.text ;TRANSMEMBRANE, DISEASE, MIGRAINE, TRAFFICKING, FOLDING, GPCR, CLR, CRLR, CGRP, ENDOPLASMIC RETICULUM, BIBN4096BS, GLYCOSYLATION, ADRENOMEDULIN, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, PROTEIN TRANSPORT ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLN A 9 ? LEU A 20 ? GLN A 28 LEU A 39 1 ? 12 HELX_P HELX_P2 2 LEU A 20 ? GLY A 33 ? LEU A 39 GLY A 52 1 ? 14 HELX_P HELX_P3 3 GLU A 34 ? TRP A 37 ? GLU A 53 TRP A 56 5 ? 4 HELX_P HELX_P4 4 ASP A 39 ? GLY A 62 ? ASP A 58 GLY A 81 1 ? 24 HELX_P HELX_P5 5 ASN A 67 ? PHE A 82 ? ASN A 86 PHE A 101 1 ? 16 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf1 disulf ? ? A CYS 8 SG ? ? ? 1_555 A CYS 63 SG ? ? A CYS 27 A CYS 82 1_555 ? ? ? ? ? ? ? 2.028 ? disulf2 disulf ? ? A CYS 21 SG ? ? ? 1_555 A CYS 53 SG ? ? A CYS 40 A CYS 72 1_555 ? ? ? ? ? ? ? 2.029 ? disulf3 disulf ? ? A CYS 38 SG ? ? ? 1_555 A CYS 85 SG ? ? A CYS 57 A CYS 104 1_555 ? ? ? ? ? ? ? 2.033 ? covale1 covale ? ? A ASP 28 C ? ? ? 1_555 A MSE 29 N ? ? A ASP 47 A MSE 48 1_555 ? ? ? ? ? ? ? 1.329 ? covale2 covale ? ? A MSE 29 C ? ? ? 1_555 A GLU 30 N ? ? A MSE 48 A GLU 49 1_555 ? ? ? ? ? ? ? 1.326 ? covale3 covale ? ? A HIS 56 C ? ? ? 1_555 A MSE 57 N ? ? A HIS 75 A MSE 76 1_555 ? ? ? ? ? ? ? 1.330 ? covale4 covale ? ? A MSE 57 C ? ? ? 1_555 A ALA 58 N ? ? A MSE 76 A ALA 77 1_555 ? ? ? ? ? ? ? 1.333 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id TRP _struct_mon_prot_cis.label_seq_id 65 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id TRP _struct_mon_prot_cis.auth_seq_id 84 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 66 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 85 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -0.39 # _database_PDB_matrix.entry_id 2YX8 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2YX8 _atom_sites.fract_transf_matrix[1][1] 0.023203 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.023203 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.012049 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 20 ? ? ? A . n A 1 2 SER 2 21 ? ? ? A . n A 1 3 PHE 3 22 ? ? ? A . n A 1 4 THR 4 23 ? ? ? A . n A 1 5 SER 5 24 ? ? ? A . n A 1 6 SER 6 25 ? ? ? A . n A 1 7 GLY 7 26 ? ? ? A . n A 1 8 CYS 8 27 27 CYS CYS A . n A 1 9 GLN 9 28 28 GLN GLN A . n A 1 10 GLU 10 29 29 GLU GLU A . n A 1 11 ALA 11 30 30 ALA ALA A . n A 1 12 ASN 12 31 31 ASN ASN A . n A 1 13 TYR 13 32 32 TYR TYR A . n A 1 14 GLY 14 33 33 GLY GLY A . n A 1 15 ALA 15 34 34 ALA ALA A . n A 1 16 LEU 16 35 35 LEU LEU A . n A 1 17 LEU 17 36 36 LEU LEU A . n A 1 18 ARG 18 37 37 ARG ARG A . n A 1 19 GLU 19 38 38 GLU GLU A . n A 1 20 LEU 20 39 39 LEU LEU A . n A 1 21 CYS 21 40 40 CYS CYS A . n A 1 22 LEU 22 41 41 LEU LEU A . n A 1 23 THR 23 42 42 THR THR A . n A 1 24 GLN 24 43 43 GLN GLN A . n A 1 25 PHE 25 44 44 PHE PHE A . n A 1 26 GLN 26 45 45 GLN GLN A . n A 1 27 VAL 27 46 46 VAL VAL A . n A 1 28 ASP 28 47 47 ASP ASP A . n A 1 29 MSE 29 48 48 MSE MSE A . n A 1 30 GLU 30 49 49 GLU GLU A . n A 1 31 ALA 31 50 50 ALA ALA A . n A 1 32 VAL 32 51 51 VAL VAL A . n A 1 33 GLY 33 52 52 GLY GLY A . n A 1 34 GLU 34 53 53 GLU GLU A . n A 1 35 THR 35 54 54 THR THR A . n A 1 36 LEU 36 55 55 LEU LEU A . n A 1 37 TRP 37 56 56 TRP TRP A . n A 1 38 CYS 38 57 57 CYS CYS A . n A 1 39 ASP 39 58 58 ASP ASP A . n A 1 40 TRP 40 59 59 TRP TRP A . n A 1 41 GLY 41 60 60 GLY GLY A . n A 1 42 ARG 42 61 61 ARG ARG A . n A 1 43 THR 43 62 62 THR THR A . n A 1 44 ILE 44 63 63 ILE ILE A . n A 1 45 ARG 45 64 64 ARG ARG A . n A 1 46 SER 46 65 65 SER SER A . n A 1 47 TYR 47 66 66 TYR TYR A . n A 1 48 ARG 48 67 67 ARG ARG A . n A 1 49 GLU 49 68 68 GLU GLU A . n A 1 50 LEU 50 69 69 LEU LEU A . n A 1 51 ALA 51 70 70 ALA ALA A . n A 1 52 ASP 52 71 71 ASP ASP A . n A 1 53 CYS 53 72 72 CYS CYS A . n A 1 54 THR 54 73 73 THR THR A . n A 1 55 TRP 55 74 74 TRP TRP A . n A 1 56 HIS 56 75 75 HIS HIS A . n A 1 57 MSE 57 76 76 MSE MSE A . n A 1 58 ALA 58 77 77 ALA ALA A . n A 1 59 GLU 59 78 78 GLU GLU A . n A 1 60 LYS 60 79 79 LYS LYS A . n A 1 61 LEU 61 80 80 LEU LEU A . n A 1 62 GLY 62 81 81 GLY GLY A . n A 1 63 CYS 63 82 82 CYS CYS A . n A 1 64 PHE 64 83 83 PHE PHE A . n A 1 65 TRP 65 84 84 TRP TRP A . n A 1 66 PRO 66 85 85 PRO PRO A . n A 1 67 ASN 67 86 86 ASN ASN A . n A 1 68 ALA 68 87 87 ALA ALA A . n A 1 69 GLU 69 88 88 GLU GLU A . n A 1 70 VAL 70 89 89 VAL VAL A . n A 1 71 ASP 71 90 90 ASP ASP A . n A 1 72 ARG 72 91 91 ARG ARG A . n A 1 73 PHE 73 92 92 PHE PHE A . n A 1 74 PHE 74 93 93 PHE PHE A . n A 1 75 LEU 75 94 94 LEU LEU A . n A 1 76 ALA 76 95 95 ALA ALA A . n A 1 77 VAL 77 96 96 VAL VAL A . n A 1 78 HIS 78 97 97 HIS HIS A . n A 1 79 GLY 79 98 98 GLY GLY A . n A 1 80 ARG 80 99 99 ARG ARG A . n A 1 81 TYR 81 100 100 TYR TYR A . n A 1 82 PHE 82 101 101 PHE PHE A . n A 1 83 ARG 83 102 102 ARG ARG A . n A 1 84 SER 84 103 103 SER SER A . n A 1 85 CYS 85 104 104 CYS CYS A . n A 1 86 PRO 86 105 105 PRO PRO A . n A 1 87 ILE 87 106 106 ILE ILE A . n A 1 88 SER 88 107 107 SER SER A . n A 1 89 GLY 89 108 ? ? ? A . n A 1 90 ARG 90 109 ? ? ? A . n A 1 91 ALA 91 110 ? ? ? A . n A 1 92 VAL 92 111 ? ? ? A . n A 1 93 ARG 93 112 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'NPPSFA, National Project on Protein Structural and Functional Analyses' _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 113 1 HOH HOH A . B 2 HOH 2 114 2 HOH HOH A . B 2 HOH 3 115 3 HOH HOH A . B 2 HOH 4 116 4 HOH HOH A . B 2 HOH 5 117 5 HOH HOH A . B 2 HOH 6 118 6 HOH HOH A . B 2 HOH 7 119 7 HOH HOH A . B 2 HOH 8 120 8 HOH HOH A . B 2 HOH 9 121 9 HOH HOH A . B 2 HOH 10 122 10 HOH HOH A . B 2 HOH 11 123 11 HOH HOH A . B 2 HOH 12 124 12 HOH HOH A . B 2 HOH 13 125 13 HOH HOH A . B 2 HOH 14 126 14 HOH HOH A . B 2 HOH 15 127 15 HOH HOH A . B 2 HOH 16 128 16 HOH HOH A . B 2 HOH 17 129 17 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 29 A MSE 48 ? MET SELENOMETHIONINE 2 A MSE 57 A MSE 76 ? MET SELENOMETHIONINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 software_defined_assembly PISA dimeric 2 2 author_defined_assembly ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,B 2 1 A,B # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1410 ? 1 MORE -10 ? 1 'SSA (A^2)' 9690 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1.0000000000 0.0000000000 0.0000000000 43.0970000000 0.0000000000 -1.0000000000 0.0000000000 43.0970000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2008-04-29 2 'Structure model' 1 1 2011-07-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 HKL-2000 'data collection' . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 SOLVE phasing . ? 5 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 LEU A 39 ? ? -105.12 -64.89 2 1 PHE A 101 ? ? -118.31 66.80 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 20 ? A GLY 1 2 1 Y 1 A SER 21 ? A SER 2 3 1 Y 1 A PHE 22 ? A PHE 3 4 1 Y 1 A THR 23 ? A THR 4 5 1 Y 1 A SER 24 ? A SER 5 6 1 Y 1 A SER 25 ? A SER 6 7 1 Y 1 A GLY 26 ? A GLY 7 8 1 Y 1 A GLY 108 ? A GLY 89 9 1 Y 1 A ARG 109 ? A ARG 90 10 1 Y 1 A ALA 110 ? A ALA 91 11 1 Y 1 A VAL 111 ? A VAL 92 12 1 Y 1 A ARG 112 ? A ARG 93 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #