data_4DZK # _entry.id 4DZK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4DZK pdb_00004dzk 10.2210/pdb4dzk/pdb RCSB RCSB070980 ? ? WWPDB D_1000070980 ? ? # 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 2012-08-29 2 'Structure model' 1 1 2013-06-19 3 'Structure model' 1 2 2017-11-15 4 'Structure model' 1 3 2024-02-28 # _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_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Refinement description' 3 3 'Structure model' 'Source and taxonomy' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' pdbx_entity_src_syn 2 3 'Structure model' software 3 4 'Structure model' chem_comp_atom 4 4 'Structure model' chem_comp_bond 5 4 'Structure model' database_2 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_pdbx_entity_src_syn.ncbi_taxonomy_id' 2 3 'Structure model' '_pdbx_entity_src_syn.organism_scientific' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' 5 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4DZK _pdbx_database_status.recvd_initial_deposition_date 2012-03-01 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4DZL . unspecified PDB 4DZM . unspecified PDB 4DZN . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Bruning, M.' 1 'Thomson, A.R.' 2 'Zaccai, N.R.' 3 'Brady, R.L.' 4 'Woolfson, D.N.' 5 # _citation.id primary _citation.title 'A basis set of de novo coiled-coil Peptide oligomers for rational protein design and synthetic biology.' _citation.journal_abbrev 'ACS Synth Biol' _citation.journal_volume 1 _citation.page_first 240 _citation.page_last 250 _citation.year 2012 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 2161-5063 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23651206 _citation.pdbx_database_id_DOI 10.1021/sb300028q # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Fletcher, J.M.' 1 ? primary 'Boyle, A.L.' 2 ? primary 'Bruning, M.' 3 ? primary 'Bartlett, G.J.' 4 ? primary 'Vincent, T.L.' 5 ? primary 'Zaccai, N.R.' 6 ? primary 'Armstrong, C.T.' 7 ? primary 'Bromley, E.H.' 8 ? primary 'Booth, P.J.' 9 ? primary 'Brady, R.L.' 10 ? primary 'Thomson, A.R.' 11 ? primary 'Woolfson, D.N.' 12 ? # 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 'COILED-COIL PEPTIDE CC-TRI-N13' 3431.996 1 ? ? ? ? 2 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 3 water nat water 18.015 14 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GEIAAIKQEIAANKKEIAAIKWEIAAIKQGYG _entity_poly.pdbx_seq_one_letter_code_can GEIAAIKQEIAANKKEIAAIKWEIAAIKQGYG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CHLORIDE ION' CL 3 water HOH # 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 GLU n 1 3 ILE n 1 4 ALA n 1 5 ALA n 1 6 ILE n 1 7 LYS n 1 8 GLN n 1 9 GLU n 1 10 ILE n 1 11 ALA n 1 12 ALA n 1 13 ASN n 1 14 LYS n 1 15 LYS n 1 16 GLU n 1 17 ILE n 1 18 ALA n 1 19 ALA n 1 20 ILE n 1 21 LYS n 1 22 TRP n 1 23 GLU n 1 24 ILE n 1 25 ALA n 1 26 ALA n 1 27 ILE n 1 28 LYS n 1 29 GLN n 1 30 GLY n 1 31 TYR n 1 32 GLY 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _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 'Solid state peptide synthesis' # 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 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # 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 1 1 GLY GLY A . n A 1 2 GLU 2 2 2 GLU GLU A . n A 1 3 ILE 3 3 3 ILE ILE A . n A 1 4 ALA 4 4 4 ALA ALA A . n A 1 5 ALA 5 5 5 ALA ALA A . n A 1 6 ILE 6 6 6 ILE ILE A . n A 1 7 LYS 7 7 7 LYS LYS A . n A 1 8 GLN 8 8 8 GLN GLN A . n A 1 9 GLU 9 9 9 GLU GLU A . n A 1 10 ILE 10 10 10 ILE ILE A . n A 1 11 ALA 11 11 11 ALA ALA A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 ASN 13 13 13 ASN ASN A . n A 1 14 LYS 14 14 14 LYS LYS A . n A 1 15 LYS 15 15 15 LYS LYS A . n A 1 16 GLU 16 16 16 GLU GLU A . n A 1 17 ILE 17 17 17 ILE ILE A . n A 1 18 ALA 18 18 18 ALA ALA A . n A 1 19 ALA 19 19 19 ALA ALA A . n A 1 20 ILE 20 20 20 ILE ILE A . n A 1 21 LYS 21 21 21 LYS LYS A . n A 1 22 TRP 22 22 22 TRP TRP A . n A 1 23 GLU 23 23 23 GLU GLU A . n A 1 24 ILE 24 24 24 ILE ILE A . n A 1 25 ALA 25 25 25 ALA ALA A . n A 1 26 ALA 26 26 26 ALA ALA A . n A 1 27 ILE 27 27 27 ILE ILE A . n A 1 28 LYS 28 28 28 LYS LYS A . n A 1 29 GLN 29 29 29 GLN GLN A . n A 1 30 GLY 30 30 ? ? ? A . n A 1 31 TYR 31 31 ? ? ? A . n A 1 32 GLY 32 32 ? ? ? A . 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 B 2 CL 1 101 1 CL CL A . C 3 HOH 1 201 2 HOH HOH A . C 3 HOH 2 202 5 HOH HOH A . C 3 HOH 3 203 6 HOH HOH A . C 3 HOH 4 204 9 HOH HOH A . C 3 HOH 5 205 11 HOH HOH A . C 3 HOH 6 206 12 HOH HOH A . C 3 HOH 7 207 13 HOH HOH A . C 3 HOH 8 208 14 HOH HOH A . C 3 HOH 9 209 15 HOH HOH A . C 3 HOH 10 210 16 HOH HOH A . C 3 HOH 11 211 17 HOH HOH A . C 3 HOH 12 212 18 HOH HOH A . C 3 HOH 13 213 19 HOH HOH A . C 3 HOH 14 214 21 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PHASER phasing . ? 1 REFMAC refinement 5.5.0102 ? 2 MOSFLM 'data reduction' . ? 3 SCALA 'data scaling' . ? 4 # _cell.entry_id 4DZK _cell.length_a 38.150 _cell.length_b 38.150 _cell.length_c 44.300 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 4DZK _symmetry.space_group_name_H-M 'P 3 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4DZK _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.71 _exptl_crystal.density_percent_sol 54.64 _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.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details '2.0 M (NH4)2SO4, 5 % v/v 2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 291K' _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 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2010-02-20 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.98 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I02' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I02 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.98 # _reflns.entry_id 4DZK _reflns.observed_criterion_sigma_I 7.1 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 44.3 _reflns.d_resolution_high 1.79 _reflns.number_obs 3777 _reflns.number_all ? _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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 1.8 _reflns_shell.d_res_low 1.9 _reflns_shell.percent_possible_all 100.00 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _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_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4DZK _refine.ls_number_reflns_obs 3607 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 44.30 _refine.ls_d_res_high 1.79 _refine.ls_percent_reflns_obs 99.37 _refine.ls_R_factor_obs 0.23174 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23019 _refine.ls_R_factor_R_free 0.26899 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.5 _refine.ls_number_reflns_R_free 168 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.914 _refine.correlation_coeff_Fo_to_Fc_free 0.901 _refine.B_iso_mean 21.455 _refine.aniso_B[1][1] 12.46 _refine.aniso_B[2][2] 12.46 _refine.aniso_B[3][3] -24.92 _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 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.026 _refine.pdbx_overall_ESU_R_Free 0.027 _refine.overall_SU_ML 0.083 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 3.013 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 221 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 14 _refine_hist.number_atoms_total 236 _refine_hist.d_res_high 1.79 _refine_hist.d_res_low 44.30 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.007 0.023 ? 223 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.001 0.020 ? 153 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.033 1.942 ? 297 ? 'X-RAY DIFFRACTION' r_angle_other_deg 2.856 3.000 ? 385 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 3.932 5.000 ? 28 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 43.024 28.750 ? 8 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 18.948 15.000 ? 49 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_chiral_restr 0.043 0.200 ? 35 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.002 0.020 ? 234 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.001 0.020 ? 33 ? 'X-RAY DIFFRACTION' r_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_it 2.637 8.000 ? 143 ? 'X-RAY DIFFRACTION' r_mcbond_other 0.756 8.000 ? 58 ? 'X-RAY DIFFRACTION' r_mcangle_it 3.982 12.000 ? 225 ? 'X-RAY DIFFRACTION' r_scbond_it 7.437 16.000 ? 80 ? 'X-RAY DIFFRACTION' r_scangle_it 11.535 24.000 ? 72 ? 'X-RAY DIFFRACTION' r_rigid_bond_restr ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_free ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded ? ? ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.786 _refine_ls_shell.d_res_low 1.832 _refine_ls_shell.number_reflns_R_work 261 _refine_ls_shell.R_factor_R_work 0.156 _refine_ls_shell.percent_reflns_obs 98.21 _refine_ls_shell.R_factor_R_free 0.353 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 13 _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' # _database_PDB_matrix.entry_id 4DZK _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 # _struct.entry_id 4DZK _struct.title 'A de novo designed Coiled Coil CC-Tri-N13' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4DZK _struct_keywords.pdbx_keywords 'DE NOVO PROTEIN' _struct_keywords.text '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 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4DZK _struct_ref.pdbx_db_accession 4DZK _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code GEIAAIKQEIAANKKEIAAIKWEIAAIKQGYG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4DZK _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 32 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4DZK _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 32 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 32 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # 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)' 3500 ? 1 MORE -46 ? 1 'SSA (A^2)' 5630 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C # 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_545 -y,x-y-1,z -0.5000000000 -0.8660254038 0.0000000000 19.0750000000 0.8660254038 -0.5000000000 0.0000000000 -33.0388691544 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5000000000 0.8660254038 0.0000000000 38.1500000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id GLY _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 1 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id GLN _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 29 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id GLY _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 1 _struct_conf.end_auth_comp_id GLN _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 29 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 29 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id CL _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 3 _struct_site.details 'BINDING SITE FOR RESIDUE CL A 101' # 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 ASN A 13 ? ASN A 13 . ? 1_555 ? 2 AC1 3 ASN A 13 ? ASN A 13 . ? 2_545 ? 3 AC1 3 ASN A 13 ? ASN A 13 . ? 3_655 ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id CL _pdbx_struct_special_symmetry.auth_seq_id 101 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id CL _pdbx_struct_special_symmetry.label_seq_id . # 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 30 ? A GLY 30 2 1 Y 1 A TYR 31 ? A TYR 31 3 1 Y 1 A GLY 32 ? A GLY 32 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ASN N N N N 14 ASN CA C N S 15 ASN C C N N 16 ASN O O N N 17 ASN CB C N N 18 ASN CG C N N 19 ASN OD1 O N N 20 ASN ND2 N N N 21 ASN OXT O N N 22 ASN H H N N 23 ASN H2 H N N 24 ASN HA H N N 25 ASN HB2 H N N 26 ASN HB3 H N N 27 ASN HD21 H N N 28 ASN HD22 H N N 29 ASN HXT H N N 30 CL CL CL N N 31 GLN N N N N 32 GLN CA C N S 33 GLN C C N N 34 GLN O O N N 35 GLN CB C N N 36 GLN CG C N N 37 GLN CD C N N 38 GLN OE1 O N N 39 GLN NE2 N N N 40 GLN OXT O N N 41 GLN H H N N 42 GLN H2 H N N 43 GLN HA H N N 44 GLN HB2 H N N 45 GLN HB3 H N N 46 GLN HG2 H N N 47 GLN HG3 H N N 48 GLN HE21 H N N 49 GLN HE22 H N N 50 GLN HXT H N N 51 GLU N N N N 52 GLU CA C N S 53 GLU C C N N 54 GLU O O N N 55 GLU CB C N N 56 GLU CG C N N 57 GLU CD C N N 58 GLU OE1 O N N 59 GLU OE2 O N N 60 GLU OXT O N N 61 GLU H H N N 62 GLU H2 H N N 63 GLU HA H N N 64 GLU HB2 H N N 65 GLU HB3 H N N 66 GLU HG2 H N N 67 GLU HG3 H N N 68 GLU HE2 H N N 69 GLU HXT H N N 70 GLY N N N N 71 GLY CA C N N 72 GLY C C N N 73 GLY O O N N 74 GLY OXT O N N 75 GLY H H N N 76 GLY H2 H N N 77 GLY HA2 H N N 78 GLY HA3 H N N 79 GLY HXT H N N 80 HOH O O N N 81 HOH H1 H N N 82 HOH H2 H N N 83 ILE N N N N 84 ILE CA C N S 85 ILE C C N N 86 ILE O O N N 87 ILE CB C N S 88 ILE CG1 C N N 89 ILE CG2 C N N 90 ILE CD1 C N N 91 ILE OXT O N N 92 ILE H H N N 93 ILE H2 H N N 94 ILE HA H N N 95 ILE HB H N N 96 ILE HG12 H N N 97 ILE HG13 H N N 98 ILE HG21 H N N 99 ILE HG22 H N N 100 ILE HG23 H N N 101 ILE HD11 H N N 102 ILE HD12 H N N 103 ILE HD13 H N N 104 ILE HXT H N N 105 LYS N N N N 106 LYS CA C N S 107 LYS C C N N 108 LYS O O N N 109 LYS CB C N N 110 LYS CG C N N 111 LYS CD C N N 112 LYS CE C N N 113 LYS NZ N N N 114 LYS OXT O N N 115 LYS H H N N 116 LYS H2 H N N 117 LYS HA H N N 118 LYS HB2 H N N 119 LYS HB3 H N N 120 LYS HG2 H N N 121 LYS HG3 H N N 122 LYS HD2 H N N 123 LYS HD3 H N N 124 LYS HE2 H N N 125 LYS HE3 H N N 126 LYS HZ1 H N N 127 LYS HZ2 H N N 128 LYS HZ3 H N N 129 LYS HXT H N N 130 TRP N N N N 131 TRP CA C N S 132 TRP C C N N 133 TRP O O N N 134 TRP CB C N N 135 TRP CG C Y N 136 TRP CD1 C Y N 137 TRP CD2 C Y N 138 TRP NE1 N Y N 139 TRP CE2 C Y N 140 TRP CE3 C Y N 141 TRP CZ2 C Y N 142 TRP CZ3 C Y N 143 TRP CH2 C Y N 144 TRP OXT O N N 145 TRP H H N N 146 TRP H2 H N N 147 TRP HA H N N 148 TRP HB2 H N N 149 TRP HB3 H N N 150 TRP HD1 H N N 151 TRP HE1 H N N 152 TRP HE3 H N N 153 TRP HZ2 H N N 154 TRP HZ3 H N N 155 TRP HH2 H N N 156 TRP HXT H N N 157 TYR N N N N 158 TYR CA C N S 159 TYR C C N N 160 TYR O O N N 161 TYR CB C N N 162 TYR CG C Y N 163 TYR CD1 C Y N 164 TYR CD2 C Y N 165 TYR CE1 C Y N 166 TYR CE2 C Y N 167 TYR CZ C Y N 168 TYR OH O N N 169 TYR OXT O N N 170 TYR H H N N 171 TYR H2 H N N 172 TYR HA H N N 173 TYR HB2 H N N 174 TYR HB3 H N N 175 TYR HD1 H N N 176 TYR HD2 H N N 177 TYR HE1 H N N 178 TYR HE2 H N N 179 TYR HH H N N 180 TYR HXT H N N 181 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ASN N CA sing N N 13 ASN N H sing N N 14 ASN N H2 sing N N 15 ASN CA C sing N N 16 ASN CA CB sing N N 17 ASN CA HA sing N N 18 ASN C O doub N N 19 ASN C OXT sing N N 20 ASN CB CG sing N N 21 ASN CB HB2 sing N N 22 ASN CB HB3 sing N N 23 ASN CG OD1 doub N N 24 ASN CG ND2 sing N N 25 ASN ND2 HD21 sing N N 26 ASN ND2 HD22 sing N N 27 ASN OXT HXT sing N N 28 GLN N CA sing N N 29 GLN N H sing N N 30 GLN N H2 sing N N 31 GLN CA C sing N N 32 GLN CA CB sing N N 33 GLN CA HA sing N N 34 GLN C O doub N N 35 GLN C OXT sing N N 36 GLN CB CG sing N N 37 GLN CB HB2 sing N N 38 GLN CB HB3 sing N N 39 GLN CG CD sing N N 40 GLN CG HG2 sing N N 41 GLN CG HG3 sing N N 42 GLN CD OE1 doub N N 43 GLN CD NE2 sing N N 44 GLN NE2 HE21 sing N N 45 GLN NE2 HE22 sing N N 46 GLN OXT HXT sing N N 47 GLU N CA sing N N 48 GLU N H sing N N 49 GLU N H2 sing N N 50 GLU CA C sing N N 51 GLU CA CB sing N N 52 GLU CA HA sing N N 53 GLU C O doub N N 54 GLU C OXT sing N N 55 GLU CB CG sing N N 56 GLU CB HB2 sing N N 57 GLU CB HB3 sing N N 58 GLU CG CD sing N N 59 GLU CG HG2 sing N N 60 GLU CG HG3 sing N N 61 GLU CD OE1 doub N N 62 GLU CD OE2 sing N N 63 GLU OE2 HE2 sing N N 64 GLU OXT HXT sing N N 65 GLY N CA sing N N 66 GLY N H sing N N 67 GLY N H2 sing N N 68 GLY CA C sing N N 69 GLY CA HA2 sing N N 70 GLY CA HA3 sing N N 71 GLY C O doub N N 72 GLY C OXT sing N N 73 GLY OXT HXT sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 ILE N CA sing N N 77 ILE N H sing N N 78 ILE N H2 sing N N 79 ILE CA C sing N N 80 ILE CA CB sing N N 81 ILE CA HA sing N N 82 ILE C O doub N N 83 ILE C OXT sing N N 84 ILE CB CG1 sing N N 85 ILE CB CG2 sing N N 86 ILE CB HB sing N N 87 ILE CG1 CD1 sing N N 88 ILE CG1 HG12 sing N N 89 ILE CG1 HG13 sing N N 90 ILE CG2 HG21 sing N N 91 ILE CG2 HG22 sing N N 92 ILE CG2 HG23 sing N N 93 ILE CD1 HD11 sing N N 94 ILE CD1 HD12 sing N N 95 ILE CD1 HD13 sing N N 96 ILE OXT HXT sing N N 97 LYS N CA sing N N 98 LYS N H sing N N 99 LYS N H2 sing N N 100 LYS CA C sing N N 101 LYS CA CB sing N N 102 LYS CA HA sing N N 103 LYS C O doub N N 104 LYS C OXT sing N N 105 LYS CB CG sing N N 106 LYS CB HB2 sing N N 107 LYS CB HB3 sing N N 108 LYS CG CD sing N N 109 LYS CG HG2 sing N N 110 LYS CG HG3 sing N N 111 LYS CD CE sing N N 112 LYS CD HD2 sing N N 113 LYS CD HD3 sing N N 114 LYS CE NZ sing N N 115 LYS CE HE2 sing N N 116 LYS CE HE3 sing N N 117 LYS NZ HZ1 sing N N 118 LYS NZ HZ2 sing N N 119 LYS NZ HZ3 sing N N 120 LYS OXT HXT sing N N 121 TRP N CA sing N N 122 TRP N H sing N N 123 TRP N H2 sing N N 124 TRP CA C sing N N 125 TRP CA CB sing N N 126 TRP CA HA sing N N 127 TRP C O doub N N 128 TRP C OXT sing N N 129 TRP CB CG sing N N 130 TRP CB HB2 sing N N 131 TRP CB HB3 sing N N 132 TRP CG CD1 doub Y N 133 TRP CG CD2 sing Y N 134 TRP CD1 NE1 sing Y N 135 TRP CD1 HD1 sing N N 136 TRP CD2 CE2 doub Y N 137 TRP CD2 CE3 sing Y N 138 TRP NE1 CE2 sing Y N 139 TRP NE1 HE1 sing N N 140 TRP CE2 CZ2 sing Y N 141 TRP CE3 CZ3 doub Y N 142 TRP CE3 HE3 sing N N 143 TRP CZ2 CH2 doub Y N 144 TRP CZ2 HZ2 sing N N 145 TRP CZ3 CH2 sing Y N 146 TRP CZ3 HZ3 sing N N 147 TRP CH2 HH2 sing N N 148 TRP OXT HXT sing N N 149 TYR N CA sing N N 150 TYR N H sing N N 151 TYR N H2 sing N N 152 TYR CA C sing N N 153 TYR CA CB sing N N 154 TYR CA HA sing N N 155 TYR C O doub N N 156 TYR C OXT sing N N 157 TYR CB CG sing N N 158 TYR CB HB2 sing N N 159 TYR CB HB3 sing N N 160 TYR CG CD1 doub Y N 161 TYR CG CD2 sing Y N 162 TYR CD1 CE1 sing Y N 163 TYR CD1 HD1 sing N N 164 TYR CD2 CE2 doub Y N 165 TYR CD2 HD2 sing N N 166 TYR CE1 CZ doub Y N 167 TYR CE1 HE1 sing N N 168 TYR CE2 CZ sing Y N 169 TYR CE2 HE2 sing N N 170 TYR CZ OH sing N N 171 TYR OH HH sing N N 172 TYR OXT HXT sing N N 173 # loop_ _pdbx_reflns_twin.domain_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.type _pdbx_reflns_twin.operator _pdbx_reflns_twin.fraction 1 1 1 ? 'H, K, L' 0.571 2 1 1 ? -h,-k,l 0.429 # _atom_sites.entry_id 4DZK _atom_sites.fract_transf_matrix[1][1] 0.026212 _atom_sites.fract_transf_matrix[1][2] 0.015134 _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] 0.030267 _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] 0.022573 _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 CL N O # loop_