data_6UF4 # _entry.id 6UF4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.336 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 6UF4 WWPDB D_1000244514 # _pdbx_database_related.db_name PDB _pdbx_database_related.details 'same peptide, different crystal form' _pdbx_database_related.db_id 6UDZ _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6UF4 _pdbx_database_status.recvd_initial_deposition_date 2019-09-23 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Mulligan, V.K.' 1 0000-0001-6038-8922 'Kang, C.S.' 2 0000-0003-0959-0783 'Antselovich, I.' 3 0000-0002-2208-9937 'Sawaya, M.R.' 4 0000-0003-0874-9043 'Yeates, T.O.' 5 0000-0001-5709-9839 'Baker, D.' 6 0000-0001-7896-6217 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Protein Sci.' _citation.journal_id_ASTM PRCIEI _citation.journal_id_CSD 0795 _citation.journal_id_ISSN 1469-896X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 29 _citation.language ? _citation.page_first 2433 _citation.page_last 2445 _citation.title 'Computational design of mixed chirality peptide macrocycles with internal symmetry.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/pro.3974 _citation.pdbx_database_id_PubMed 33058266 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mulligan, V.K.' 1 0000-0001-6038-8922 primary 'Kang, C.S.' 2 0000-0003-0959-0783 primary 'Sawaya, M.R.' 3 ? primary 'Rettie, S.' 4 ? primary 'Li, X.' 5 ? primary 'Antselovich, I.' 6 ? primary 'Craven, T.W.' 7 ? primary 'Watkins, A.M.' 8 ? primary 'Labonte, J.W.' 9 ? primary 'DiMaio, F.' 10 ? primary 'Yeates, T.O.' 11 0000-0001-5709-9839 primary 'Baker, D.' 12 ? # _cell.angle_alpha 102.310 _cell.angle_alpha_esd ? _cell.angle_beta 106.340 _cell.angle_beta_esd ? _cell.angle_gamma 86.240 _cell.angle_gamma_esd ? _cell.entry_id 6UF4 _cell.details ? _cell.formula_units_Z ? _cell.length_a 14.150 _cell.length_a_esd ? _cell.length_b 16.410 _cell.length_b_esd ? _cell.length_c 16.560 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UF4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 2 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P -1' _symmetry.pdbx_full_space_group_name_H-M ? # 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 syn 'S2-4, Pusgley crystal form 2' 1120.316 2 ? ? ? 'The asymmetric unit contains half of the molecule. The second half is generated by a crystallographic symmetry operator.' 2 water nat water 18.015 17 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(D)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'E(DPR)(DPR)K(DVA)(DGL)PP(DLY)V' _entity_poly.pdbx_seq_one_letter_code_can EPPKVEPPKV _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLU n 1 2 DPR n 1 3 DPR n 1 4 LYS n 1 5 DVA n 1 6 DGL n 1 7 PRO n 1 8 PRO n 1 9 DLY n 1 10 VAL n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 10 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details 'ab initio design' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6UF4 _struct_ref.pdbx_db_accession 6UF4 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 6UF4 A 1 ? 10 ? 6UF4 1 ? 10 ? 1 10 2 1 6UF4 B 1 ? 10 ? 6UF4 1 ? 10 ? 1 10 # 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 DGL 'D-peptide linking' . 'D-GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 DLY 'D-peptide linking' . D-LYSINE ? 'C6 H14 N2 O2' 146.188 DPR 'D-peptide linking' . D-PROLINE ? 'C5 H9 N O2' 115.130 DVA 'D-peptide linking' . D-VALINE ? 'C5 H11 N O2' 117.146 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 HOH non-polymer . WATER ? 'H2 O' 18.015 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 6UF4 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.58 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 22.25 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '2.4 M sodium malonate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2018-03-22 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Si (111)' _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97918 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 24-ID-E' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97918 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 24-ID-E _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 0.680 _reflns.entry_id 6UF4 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.100 _reflns.d_resolution_low 16.033 _reflns.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.number_all ? _reflns.number_obs 5355 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 94.300 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 5.815 _reflns.pdbx_Rmerge_I_obs 0.059 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 19.140 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.992 _reflns.pdbx_scaling_rejects 200 _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.065 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 31141 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.995 _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 1.100 1.130 ? 15.050 ? ? ? ? 350 90.000 ? ? ? ? 0.048 ? ? ? ? ? ? ? ? 4.891 ? ? ? ? 0.054 ? ? 1 1 0.998 ? 1.130 1.160 ? 17.000 ? ? ? ? 431 99.300 ? ? ? ? 0.050 ? ? ? ? ? ? ? ? 5.870 ? ? ? ? 0.055 ? ? 2 1 0.998 ? 1.160 1.190 ? 18.700 ? ? ? ? 381 97.900 ? ? ? ? 0.051 ? ? ? ? ? ? ? ? 6.052 ? ? ? ? 0.056 ? ? 3 1 0.998 ? 1.190 1.230 ? 18.550 ? ? ? ? 397 100.000 ? ? ? ? 0.052 ? ? ? ? ? ? ? ? 5.924 ? ? ? ? 0.057 ? ? 4 1 0.998 ? 1.230 1.270 ? 18.570 ? ? ? ? 373 98.900 ? ? ? ? 0.052 ? ? ? ? ? ? ? ? 6.123 ? ? ? ? 0.057 ? ? 5 1 0.998 ? 1.270 1.310 ? 18.030 ? ? ? ? 356 99.400 ? ? ? ? 0.055 ? ? ? ? ? ? ? ? 5.840 ? ? ? ? 0.060 ? ? 6 1 0.998 ? 1.310 1.360 ? 19.660 ? ? ? ? 352 100.00 ? ? ? ? 0.054 ? ? ? ? ? ? ? ? 6.182 ? ? ? ? 0.059 ? ? 7 1 0.997 ? 1.360 1.420 ? 20.330 ? ? ? ? 338 98.300 ? ? ? ? 0.054 ? ? ? ? ? ? ? ? 6.331 ? ? ? ? 0.059 ? ? 8 1 0.995 ? 1.420 1.480 ? 20.360 ? ? ? ? 316 100.000 ? ? ? ? 0.060 ? ? ? ? ? ? ? ? 6.421 ? ? ? ? 0.066 ? ? 9 1 0.996 ? 1.480 1.560 ? 21.350 ? ? ? ? 295 99.700 ? ? ? ? 0.057 ? ? ? ? ? ? ? ? 6.407 ? ? ? ? 0.062 ? ? 10 1 0.997 ? 1.560 1.640 ? 20.340 ? ? ? ? 311 99.000 ? ? ? ? 0.062 ? ? ? ? ? ? ? ? 6.273 ? ? ? ? 0.068 ? ? 11 1 0.996 ? 1.640 1.740 ? 19.730 ? ? ? ? 265 97.100 ? ? ? ? 0.062 ? ? ? ? ? ? ? ? 5.679 ? ? ? ? 0.069 ? ? 12 1 0.996 ? 1.740 1.860 ? 20.920 ? ? ? ? 257 95.900 ? ? ? ? 0.071 ? ? ? ? ? ? ? ? 5.759 ? ? ? ? 0.080 ? ? 13 1 0.992 ? 1.860 2.010 ? 21.290 ? ? ? ? 232 95.900 ? ? ? ? 0.073 ? ? ? ? ? ? ? ? 5.819 ? ? ? ? 0.083 ? ? 14 1 0.987 ? 2.010 2.200 ? 19.780 ? ? ? ? 179 86.100 ? ? ? ? 0.074 ? ? ? ? ? ? ? ? 5.291 ? ? ? ? 0.084 ? ? 15 1 0.992 ? 2.200 2.460 ? 21.410 ? ? ? ? 177 83.100 ? ? ? ? 0.072 ? ? ? ? ? ? ? ? 5.401 ? ? ? ? 0.082 ? ? 16 1 0.988 ? 2.460 2.840 ? 19.660 ? ? ? ? 142 76.300 ? ? ? ? 0.068 ? ? ? ? ? ? ? ? 4.775 ? ? ? ? 0.077 ? ? 17 1 0.991 ? 2.840 3.480 ? 16.880 ? ? ? ? 96 67.100 ? ? ? ? 0.083 ? ? ? ? ? ? ? ? 3.635 ? ? ? ? 0.099 ? ? 18 1 0.974 ? 3.480 4.920 ? 18.370 ? ? ? ? 70 58.300 ? ? ? ? 0.091 ? ? ? ? ? ? ? ? 4.057 ? ? ? ? 0.106 ? ? 19 1 0.978 ? 4.920 16.033 ? 16.700 ? ? ? ? 37 58.700 ? ? ? ? 0.106 ? ? ? ? ? ? ? ? 3.865 ? ? ? ? 0.123 ? ? 20 1 0.974 ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max 6.500 _refine.B_iso_mean 1.1780 _refine.B_iso_min 0.050 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 6UF4 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.1000 _refine.ls_d_res_low 16.0330 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 5329 _refine.ls_number_reflns_R_free 534 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 94.0900 _refine.ls_percent_reflns_R_free 10.0200 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.0882 _refine.ls_R_factor_R_free 0.1014 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.0869 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.630 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 5.4100 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.0400 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id final _refine_hist.details ? _refine_hist.d_res_high 1.1000 _refine_hist.d_res_low 16.0330 _refine_hist.number_atoms_solvent 44 _refine_hist.number_atoms_total 314 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total 0 _refine_hist.pdbx_B_iso_mean_ligand 0.88 _refine_hist.pdbx_B_iso_mean_solvent 2.32 _refine_hist.pdbx_number_atoms_protein 78 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 192 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 1.1001 1.2107 . . 136 1218 97.0000 . . . 0.0918 0.0000 0.0661 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.2107 1.3858 . . 142 1284 100.0000 . . . 0.0856 0.0000 0.0687 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.3858 1.7457 . . 140 1259 99.0000 . . . 0.0941 0.0000 0.0794 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.7457 16.033 . . 116 1034 81.0000 . . . 0.1304 0.0000 0.1298 . . . . . . . . . . # _struct.entry_id 6UF4 _struct.title 'S2 symmetric peptide design number 4 crystal form 2, Pugsley' _struct.pdbx_descriptor 'S2-4, Pusgley crystal form 2' _struct.pdbx_model_details 'S2 symmetric cyclic peptide' _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6UF4 _struct_keywords.text 'cyclic peptide, centrosymmetric macrocycle, L and D-amino acids, DE NOVO PROTEIN' _struct_keywords.pdbx_keywords 'DE NOVO PROTEIN' # 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 1 ? C N N 2 ? D N N 2 ? # 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 _struct_conn.pdbx_role covale1 covale both ? A GLU 1 C ? ? ? 1_555 A DPR 2 N ? ? A GLU 1 A DPR 2 1_555 ? ? ? ? ? ? ? 1.349 ? ? covale2 covale both ? A GLU 1 N ? ? ? 1_555 A DVA 5 C ? ? A GLU 1 A DVA 5 2_555 ? ? ? ? ? ? ? 1.359 ? ? covale3 covale both ? A DPR 2 C ? ? ? 1_555 A DPR 3 N ? ? A DPR 2 A DPR 3 1_555 ? ? ? ? ? ? ? 1.349 ? ? covale4 covale both ? A DPR 3 C ? ? ? 1_555 A LYS 4 N ? ? A DPR 3 A LYS 4 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale5 covale both ? A LYS 4 C ? ? ? 1_555 A DVA 5 N ? ? A LYS 4 A DVA 5 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale6 covale both ? B GLU 1 C ? ? ? 1_555 B DPR 2 N ? ? B GLU 1 B DPR 2 1_555 ? ? ? ? ? ? ? 1.350 ? ? covale7 covale both ? B GLU 1 N ? ? ? 1_555 B DVA 5 C ? ? B GLU 1 B DVA 5 2_665 ? ? ? ? ? ? ? 1.354 ? ? covale8 covale both ? B DPR 2 C ? ? ? 1_555 B DPR 3 N ? ? B DPR 2 B DPR 3 1_555 ? ? ? ? ? ? ? 1.350 ? ? covale9 covale both ? B DPR 3 C ? ? ? 1_555 B LYS 4 N ? ? B DPR 3 B LYS 4 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale10 covale both ? B LYS 4 C ? ? ? 1_555 B DVA 5 N ? ? B LYS 4 B DVA 5 1_555 ? ? ? ? ? ? ? 1.339 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 6UF4 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.070671 _atom_sites.fract_transf_matrix[1][2] -0.004646 _atom_sites.fract_transf_matrix[1][3] 0.020202 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.061070 _atom_sites.fract_transf_matrix[2][3] 0.012682 _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] 0.064272 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C H N O # 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 GLU 1 1 1 GLU GLU A . n A 1 2 DPR 2 2 2 DPR DPR A . n A 1 3 DPR 3 3 3 DPR DPR A . n A 1 4 LYS 4 4 4 LYS LYS A . n A 1 5 DVA 5 5 5 DVA DVA A . n A 1 6 DGL 6 6 ? ? ? A . n A 1 7 PRO 7 7 ? ? ? A . n A 1 8 PRO 8 8 ? ? ? A . n A 1 9 DLY 9 9 ? ? ? A . n A 1 10 VAL 10 10 ? ? ? A . n B 1 1 GLU 1 1 1 GLU GLU B . n B 1 2 DPR 2 2 2 DPR DPR B . n B 1 3 DPR 3 3 3 DPR DPR B . n B 1 4 LYS 4 4 4 LYS LYS B . n B 1 5 DVA 5 5 5 DVA DVA B . n B 1 6 DGL 6 6 ? ? ? B . n B 1 7 PRO 7 7 ? ? ? B . n B 1 8 PRO 8 8 ? ? ? B . n B 1 9 DLY 9 9 ? ? ? B . n B 1 10 VAL 10 10 ? ? ? B . n # 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 C 2 HOH 1 101 15 HOH HOH A . C 2 HOH 2 102 9 HOH HOH A . C 2 HOH 3 103 12 HOH HOH A . C 2 HOH 4 104 14 HOH HOH A . C 2 HOH 5 105 3 HOH HOH A . C 2 HOH 6 106 1 HOH HOH A . C 2 HOH 7 107 13 HOH HOH A . C 2 HOH 8 108 17 HOH HOH A . C 2 HOH 9 109 5 HOH HOH A . D 2 HOH 1 101 10 HOH HOH B . D 2 HOH 2 102 4 HOH HOH B . D 2 HOH 3 103 16 HOH HOH B . D 2 HOH 4 104 6 HOH HOH B . D 2 HOH 5 105 7 HOH HOH B . D 2 HOH 6 106 2 HOH HOH B . D 2 HOH 7 107 11 HOH HOH B . D 2 HOH 8 108 8 HOH HOH B . # 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 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,C 2 1,3 B,D # 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_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 3 'crystal symmetry operation' 2_665 -x+1,-y+1,-z -1.0000000000 0.0000000000 0.0000000000 15.2261232874 0.0000000000 -1.0000000000 0.0000000000 16.3746773608 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2020-12-02 # _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_details.details ? # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? 20180126 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? 20180126 2 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.16_3549 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.25 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXD ? ? ? . 5 # _pdbx_entry_details.entry_id 6UF4 _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details 'The asymmetric unit contains half of the molecule. The second half is generated by a crystallographic symmetry operator.' _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # 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 DGL 6 ? A DGL 6 2 1 Y 1 A PRO 7 ? A PRO 7 3 1 Y 1 A PRO 8 ? A PRO 8 4 1 Y 1 A DLY 9 ? A DLY 9 5 1 Y 1 A VAL 10 ? A VAL 10 6 1 Y 1 B DGL 6 ? B DGL 6 7 1 Y 1 B PRO 7 ? B PRO 7 8 1 Y 1 B PRO 8 ? B PRO 8 9 1 Y 1 B DLY 9 ? B DLY 9 10 1 Y 1 B VAL 10 ? B VAL 10 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Department of Energy (DOE, United States)' 'United States' DE-FC02-02ER63421 1 'Department of Energy (DOE, United States)' 'United States' DE-AC02-06CH11357 2 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _pdbx_struct_assembly_auth_evidence.id _pdbx_struct_assembly_auth_evidence.assembly_id _pdbx_struct_assembly_auth_evidence.experimental_support _pdbx_struct_assembly_auth_evidence.details 1 1 none ? 2 2 none ? #