data_3RA3 # _entry.id 3RA3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3RA3 RCSB RCSB064679 WWPDB D_1000064679 # _pdbx_database_status.entry_id 3RA3 _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2011-03-27 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zaccai, N.R.' 1 'Sharp, T.H.' 2 'Bruning, M.' 3 'Woolfson, D.N.' 4 'Brady, R.L.' 5 # _citation.id primary _citation.title 'Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 109 _citation.page_first 13266 _citation.page_last 13271 _citation.year 2012 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22847414 _citation.pdbx_database_id_DOI 10.1073/pnas.1118622109 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Sharp, T.H.' 1 primary 'Bruning, M.' 2 primary 'Mantell, J.' 3 primary 'Sessions, R.B.' 4 primary 'Thomson, A.R.' 5 primary 'Zaccai, N.R.' 6 primary 'Brady, R.L.' 7 primary 'Verkade, P.' 8 primary 'Woolfson, D.N.' 9 # _cell.length_a 45.082 _cell.length_b 45.082 _cell.length_c 67.593 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3RA3 _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _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.space_group_name_H-M 'P 32' _symmetry.entry_id 3RA3 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 145 _symmetry.cell_setting ? _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 syn p1c 3287.498 2 ? ? ? ? 2 polymer syn p2f 3331.928 2 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 4 water nat water 18.015 34 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no yes 'EIDALE(PHI)ENDALEQKIAALKQKIASLKQ' EIDALEFENDALEQKIAALKQKIASLKQ A,E ? 2 'polypeptide(L)' no no KIRRLKQKNARLKQEIAALEYEIAALEQ KIRRLKQKNARLKQEIAALEYEIAALEQ B,D ? # 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 ILE n 1 3 ASP n 1 4 ALA n 1 5 LEU n 1 6 GLU n 1 7 PHI n 1 8 GLU n 1 9 ASN n 1 10 ASP n 1 11 ALA n 1 12 LEU n 1 13 GLU n 1 14 GLN n 1 15 LYS n 1 16 ILE n 1 17 ALA n 1 18 ALA n 1 19 LEU n 1 20 LYS n 1 21 GLN n 1 22 LYS n 1 23 ILE n 1 24 ALA n 1 25 SER n 1 26 LEU n 1 27 LYS n 1 28 GLN n 2 1 LYS n 2 2 ILE n 2 3 ARG n 2 4 ARG n 2 5 LEU n 2 6 LYS n 2 7 GLN n 2 8 LYS n 2 9 ASN n 2 10 ALA n 2 11 ARG n 2 12 LEU n 2 13 LYS n 2 14 GLN n 2 15 GLU n 2 16 ILE n 2 17 ALA n 2 18 ALA n 2 19 LEU n 2 20 GLU n 2 21 TYR n 2 22 GLU n 2 23 ILE n 2 24 ALA n 2 25 ALA n 2 26 LEU n 2 27 GLU n 2 28 GLN n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? 'Peptide synthesis was carried out according to standard Fmoc SPPS protocols' 2 1 sample ? ? ? ? ? 'Peptide synthesis was carried out according to standard Fmoc SPPS protocols' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 3RA3 3RA3 1 ? ? ? 2 PDB 3RA3 3RA3 2 ? ? ? # 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 3RA3 A 1 ? 28 ? 3RA3 1 ? 28 ? 1 28 2 1 3RA3 E 1 ? 28 ? 3RA3 1 ? 28 ? 1 28 3 2 3RA3 B 1 ? 28 ? 3RA3 1 ? 28 ? 1 28 4 2 3RA3 D 1 ? 28 ? 3RA3 1 ? 28 ? 1 28 # 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 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 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 PHI 'L-peptide linking' n IODO-PHENYLALANINE ? 'C9 H10 I N O2' 291.086 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # _exptl.crystals_number 1 _exptl.entry_id 3RA3 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 3.00 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 58.94 _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 4.5 _exptl_crystal_grow.temp 291 _exptl_crystal_grow.pdbx_details '0.2M zinc acetate, 0.1M sodium acetate, 10%(w/v) PEG 3K, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.7 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I04' _diffrn_source.pdbx_wavelength_list 1.7 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I04 # _reflns.entry_id 3RA3 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 2.3 _reflns.d_resolution_low 25 _reflns.number_all ? _reflns.number_obs 6777 _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs 0.102 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 21 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.2 _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.30 _reflns_shell.d_res_low 2.38 _reflns_shell.percent_possible_obs ? _reflns_shell.percent_possible_all 98.8 _reflns_shell.Rmerge_I_obs 0.606 _reflns_shell.meanI_over_sigI_obs 1.95 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_redundancy 5 _reflns_shell.number_unique_all 1388 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3RA3 _refine.ls_d_res_high 2.3100 _refine.ls_d_res_low 22.5400 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.8100 _refine.ls_number_reflns_obs 6762 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'U VALUES: REFINED INDIVIDUALLY' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1941 _refine.ls_R_factor_R_work 0.1882 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2480 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 10.4000 _refine.ls_number_reflns_R_free 701 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 45.7517 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 5.0400 _refine.aniso_B[2][2] 5.0400 _refine.aniso_B[3][3] -10.0800 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9450 _refine.correlation_coeff_Fo_to_Fc_free 0.9020 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free 0.0470 _refine.overall_SU_ML 0.1660 _refine.overall_SU_B 7.0580 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 85.030 _refine.B_iso_min 26.030 _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 857 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 34 _refine_hist.number_atoms_total 892 _refine_hist.d_res_high 2.3100 _refine_hist.d_res_low 22.5400 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 857 0.020 0.022 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1140 1.816 2.030 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 102 6.526 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 42 38.388 26.667 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 188 21.487 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 6 10.957 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 133 0.104 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 606 0.007 0.020 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 526 1.030 1.500 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 827 2.034 2.000 ? ? 'X-RAY DIFFRACTION' r_scbond_it 331 3.561 3.000 ? ? 'X-RAY DIFFRACTION' r_scangle_it 313 6.262 4.500 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 2.3070 _refine_ls_shell.d_res_low 2.3670 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 97.5300 _refine_ls_shell.number_reflns_R_work 464 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2310 _refine_ls_shell.R_factor_R_free 0.3640 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 49 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 513 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.redundancy_reflns_obs ? # _struct.entry_id 3RA3 _struct.title 'Crystal structure of a section of a de novo design gigaDalton protein fibre' _struct.pdbx_descriptor 'p1c, p2f' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3RA3 _struct_keywords.text 'coiled coil domain, fiber, KIH interactions, synthetic biology, helical reconstruction, 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 2 ? C N N 2 ? D N N 1 ? E N N 3 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 4 ? # _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 ASP A 3 ? GLN A 28 ? ASP A 3 GLN A 28 1 ? 26 HELX_P HELX_P2 2 ARG B 3 ? GLU B 27 ? ARG B 3 GLU B 27 1 ? 25 HELX_P HELX_P3 3 ILE C 2 ? GLU C 27 ? ILE D 2 GLU D 27 1 ? 26 HELX_P HELX_P4 4 ALA D 4 ? ILE D 23 ? ALA E 4 ILE E 23 1 ? 20 # _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 covale1 covale ? ? A GLU 6 C ? ? ? 1_555 A PHI 7 N ? ? A GLU 6 A PHI 7 1_555 ? ? ? ? ? ? ? 1.321 ? covale2 covale ? ? A PHI 7 C ? ? ? 1_555 A GLU 8 N ? ? A PHI 7 A GLU 8 1_555 ? ? ? ? ? ? ? 1.331 ? covale3 covale ? ? D GLU 6 C ? ? ? 1_555 D PHI 7 N ? ? E GLU 6 E PHI 7 1_555 ? ? ? ? ? ? ? 1.324 ? covale4 covale ? ? D PHI 7 C ? ? ? 1_555 D GLU 8 N ? ? E PHI 7 E GLU 8 1_555 ? ? ? ? ? ? ? 1.326 ? metalc1 metalc ? ? D GLU 6 OE2 ? ? ? 1_555 E NA . NA ? ? E GLU 6 E NA 29 1_555 ? ? ? ? ? ? ? 2.266 ? metalc2 metalc ? ? D GLU 6 OE1 ? ? ? 1_555 E NA . NA ? ? E GLU 6 E NA 29 1_555 ? ? ? ? ? ? ? 2.435 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GLU 1 D . ? GLU 1 E ILE 2 D ? ILE 2 E 1 9.59 2 SER 25 D . ? SER 25 E LEU 26 D ? LEU 26 E 1 -17.16 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 3 _struct_site.details 'BINDING SITE FOR RESIDUE NA E 29' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 3 GLU A 6 ? GLU A 6 . ? 1_545 ? 2 AC1 3 ASP A 10 ? ASP A 10 . ? 1_545 ? 3 AC1 3 GLU D 6 ? GLU E 6 . ? 1_555 ? # _atom_sites.entry_id 3RA3 _atom_sites.fract_transf_matrix[1][1] 0.022182 _atom_sites.fract_transf_matrix[1][2] 0.012807 _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] 0.025613 _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] 0.014794 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C I N NA 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 ILE 2 2 2 ILE ILE A . n A 1 3 ASP 3 3 3 ASP ASP A . n A 1 4 ALA 4 4 4 ALA ALA A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 GLU 6 6 6 GLU GLU A . n A 1 7 PHI 7 7 7 PHI PHI A . n A 1 8 GLU 8 8 8 GLU GLU A . n A 1 9 ASN 9 9 9 ASN ASN A . n A 1 10 ASP 10 10 10 ASP ASP A . n A 1 11 ALA 11 11 11 ALA ALA A . n A 1 12 LEU 12 12 12 LEU LEU A . n A 1 13 GLU 13 13 13 GLU GLU A . n A 1 14 GLN 14 14 14 GLN GLN A . n A 1 15 LYS 15 15 15 LYS LYS A . n A 1 16 ILE 16 16 16 ILE ILE A . n A 1 17 ALA 17 17 17 ALA ALA A . n A 1 18 ALA 18 18 18 ALA ALA A . n A 1 19 LEU 19 19 19 LEU LEU A . n A 1 20 LYS 20 20 20 LYS LYS A . n A 1 21 GLN 21 21 21 GLN GLN A . n A 1 22 LYS 22 22 22 LYS LYS A . n A 1 23 ILE 23 23 23 ILE ILE A . n A 1 24 ALA 24 24 24 ALA ALA A . n A 1 25 SER 25 25 25 SER SER A . n A 1 26 LEU 26 26 26 LEU LEU A . n A 1 27 LYS 27 27 27 LYS LYS A . n A 1 28 GLN 28 28 28 GLN GLN A . n B 2 1 LYS 1 1 ? ? ? B . n B 2 2 ILE 2 2 ? ? ? B . n B 2 3 ARG 3 3 3 ARG ARG B . n B 2 4 ARG 4 4 4 ARG ARG B . n B 2 5 LEU 5 5 5 LEU LEU B . n B 2 6 LYS 6 6 6 LYS LYS B . n B 2 7 GLN 7 7 7 GLN GLN B . n B 2 8 LYS 8 8 8 LYS LYS B . n B 2 9 ASN 9 9 9 ASN ASN B . n B 2 10 ALA 10 10 10 ALA ALA B . n B 2 11 ARG 11 11 11 ARG ARG B . n B 2 12 LEU 12 12 12 LEU LEU B . n B 2 13 LYS 13 13 13 LYS LYS B . n B 2 14 GLN 14 14 14 GLN GLN B . n B 2 15 GLU 15 15 15 GLU GLU B . n B 2 16 ILE 16 16 16 ILE ILE B . n B 2 17 ALA 17 17 17 ALA ALA B . n B 2 18 ALA 18 18 18 ALA ALA B . n B 2 19 LEU 19 19 19 LEU LEU B . n B 2 20 GLU 20 20 20 GLU GLU B . n B 2 21 TYR 21 21 21 TYR TYR B . n B 2 22 GLU 22 22 22 GLU GLU B . n B 2 23 ILE 23 23 23 ILE ILE B . n B 2 24 ALA 24 24 24 ALA ALA B . n B 2 25 ALA 25 25 25 ALA ALA B . n B 2 26 LEU 26 26 26 LEU LEU B . n B 2 27 GLU 27 27 27 GLU GLU B . n B 2 28 GLN 28 28 ? ? ? B . n C 2 1 LYS 1 1 ? ? ? D . n C 2 2 ILE 2 2 2 ILE ILE D . n C 2 3 ARG 3 3 3 ARG ARG D . n C 2 4 ARG 4 4 4 ARG ARG D . n C 2 5 LEU 5 5 5 LEU LEU D . n C 2 6 LYS 6 6 6 LYS LYS D . n C 2 7 GLN 7 7 7 GLN GLN D . n C 2 8 LYS 8 8 8 LYS LYS D . n C 2 9 ASN 9 9 9 ASN ASN D . n C 2 10 ALA 10 10 10 ALA ALA D . n C 2 11 ARG 11 11 11 ARG ARG D . n C 2 12 LEU 12 12 12 LEU LEU D . n C 2 13 LYS 13 13 13 LYS LYS D . n C 2 14 GLN 14 14 14 GLN GLN D . n C 2 15 GLU 15 15 15 GLU GLU D . n C 2 16 ILE 16 16 16 ILE ILE D . n C 2 17 ALA 17 17 17 ALA ALA D . n C 2 18 ALA 18 18 18 ALA ALA D . n C 2 19 LEU 19 19 19 LEU LEU D . n C 2 20 GLU 20 20 20 GLU GLU D . n C 2 21 TYR 21 21 21 TYR TYR D . n C 2 22 GLU 22 22 22 GLU GLU D . n C 2 23 ILE 23 23 23 ILE ILE D . n C 2 24 ALA 24 24 24 ALA ALA D . n C 2 25 ALA 25 25 25 ALA ALA D . n C 2 26 LEU 26 26 26 LEU LEU D . n C 2 27 GLU 27 27 27 GLU GLU D . n C 2 28 GLN 28 28 28 GLN GLN D . n D 1 1 GLU 1 1 1 GLU GLU E . n D 1 2 ILE 2 2 2 ILE ILE E . n D 1 3 ASP 3 3 3 ASP ASP E . n D 1 4 ALA 4 4 4 ALA ALA E . n D 1 5 LEU 5 5 5 LEU LEU E . n D 1 6 GLU 6 6 6 GLU GLU E . n D 1 7 PHI 7 7 7 PHI PHI E . n D 1 8 GLU 8 8 8 GLU GLU E . n D 1 9 ASN 9 9 9 ASN ASN E . n D 1 10 ASP 10 10 10 ASP ASP E . n D 1 11 ALA 11 11 11 ALA ALA E . n D 1 12 LEU 12 12 12 LEU LEU E . n D 1 13 GLU 13 13 13 GLU GLU E . n D 1 14 GLN 14 14 14 GLN GLN E . n D 1 15 LYS 15 15 15 LYS LYS E . n D 1 16 ILE 16 16 16 ILE ILE E . n D 1 17 ALA 17 17 17 ALA ALA E . n D 1 18 ALA 18 18 18 ALA ALA E . n D 1 19 LEU 19 19 19 LEU LEU E . n D 1 20 LYS 20 20 20 LYS LYS E . n D 1 21 GLN 21 21 21 GLN GLN E . n D 1 22 LYS 22 22 22 LYS LYS E . n D 1 23 ILE 23 23 23 ILE ILE E . n D 1 24 ALA 24 24 24 ALA ALA E . n D 1 25 SER 25 25 25 SER SER E . n D 1 26 LEU 26 26 26 LEU LEU E . n D 1 27 LYS 27 27 ? ? ? E . n D 1 28 GLN 28 28 ? ? ? E . n # 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 PHI 7 A PHI 7 ? PHE IODO-PHENYLALANINE 2 D PHI 7 E PHI 7 ? PHE IODO-PHENYLALANINE # 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_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,F,G 2 1 C,D,E,H,I # 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)' 1390 ? 1 MORE -12 ? 1 'SSA (A^2)' 4400 ? 2 'ABSA (A^2)' 1400 ? 2 MORE -13 ? 2 'SSA (A^2)' 4500 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id OE2 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id D _pdbx_struct_conn_angle.ptnr1_label_comp_id GLU _pdbx_struct_conn_angle.ptnr1_label_seq_id 6 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id E _pdbx_struct_conn_angle.ptnr1_auth_comp_id GLU _pdbx_struct_conn_angle.ptnr1_auth_seq_id 6 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id NA _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id E _pdbx_struct_conn_angle.ptnr2_label_comp_id NA _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id E _pdbx_struct_conn_angle.ptnr2_auth_comp_id NA _pdbx_struct_conn_angle.ptnr2_auth_seq_id 29 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id OE1 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id D _pdbx_struct_conn_angle.ptnr3_label_comp_id GLU _pdbx_struct_conn_angle.ptnr3_label_seq_id 6 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id E _pdbx_struct_conn_angle.ptnr3_auth_comp_id GLU _pdbx_struct_conn_angle.ptnr3_auth_seq_id 6 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 55.2 _pdbx_struct_conn_angle.value_esd ? # 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 2012-08-08 2 'Structure model' 1 1 2013-06-19 # _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 'Database references' # _phasing.method SAD # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 2 REFMAC 5.5.0109 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 3 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 4 DENZO . ? ? ? ? 'data reduction' ? ? ? 5 SCALEPACK . ? ? ? ? 'data scaling' ? ? ? 6 SHELXD . ? ? ? ? phasing ? ? ? # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id SER _pdbx_validate_torsion.auth_asym_id E _pdbx_validate_torsion.auth_seq_id 25 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -160.65 _pdbx_validate_torsion.psi 66.18 # 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 B LYS 1 ? B LYS 1 2 1 Y 1 B ILE 2 ? B ILE 2 3 1 Y 1 B GLN 28 ? B GLN 28 4 1 Y 1 D LYS 1 ? C LYS 1 5 1 Y 1 E LYS 27 ? D LYS 27 6 1 Y 1 E GLN 28 ? D GLN 28 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'SODIUM ION' NA 4 water HOH # loop_ _pdbx_reflns_twin.domain_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.fraction _pdbx_reflns_twin.operator _pdbx_reflns_twin.type _pdbx_reflns_twin.mean_F_square_over_mean_F2 _pdbx_reflns_twin.mean_I2_over_mean_I_square 1 1 1 0.819 'H, K, L' ? ? ? 2 1 1 0.181 h+k,-k,-l ? ? ? # 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 E 3 NA 1 29 1 NA NA E . F 4 HOH 1 29 7 HOH HOH A . F 4 HOH 2 30 13 HOH HOH A . F 4 HOH 3 31 11 HOH HOH A . F 4 HOH 4 32 32 HOH HOH A . F 4 HOH 5 33 21 HOH HOH A . F 4 HOH 6 34 22 HOH HOH A . F 4 HOH 7 35 29 HOH HOH A . G 4 HOH 1 30 1 HOH HOH B . G 4 HOH 2 31 31 HOH HOH B . G 4 HOH 3 32 3 HOH HOH B . G 4 HOH 4 33 33 HOH HOH B . G 4 HOH 5 34 34 HOH HOH B . G 4 HOH 6 35 14 HOH HOH B . G 4 HOH 7 36 2 HOH HOH B . G 4 HOH 8 37 9 HOH HOH B . G 4 HOH 9 38 19 HOH HOH B . G 4 HOH 10 39 28 HOH HOH B . H 4 HOH 1 29 9 HOH HOH D . H 4 HOH 2 31 13 HOH HOH D . H 4 HOH 3 32 14 HOH HOH D . H 4 HOH 4 33 16 HOH HOH D . H 4 HOH 5 34 20 HOH HOH D . H 4 HOH 6 35 23 HOH HOH D . H 4 HOH 7 36 25 HOH HOH D . H 4 HOH 8 37 26 HOH HOH D . H 4 HOH 9 38 27 HOH HOH D . I 4 HOH 1 30 11 HOH HOH E . I 4 HOH 2 31 10 HOH HOH E . I 4 HOH 3 32 10 HOH HOH E . I 4 HOH 4 33 12 HOH HOH E . I 4 HOH 5 34 15 HOH HOH E . I 4 HOH 6 35 18 HOH HOH E . I 4 HOH 7 36 24 HOH HOH E . I 4 HOH 8 37 2 HOH HOH E . #