data_1IFD # _entry.id 1IFD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1IFD WWPDB D_1000174130 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1IFM . unspecified PDB 2IFM . unspecified PDB 3IFM . unspecified PDB 4IFM . unspecified PDB 1IFI . unspecified PDB 1IFJ . unspecified PDB 1IFK . unspecified PDB 1IFL . unspecified PDB 1IFN . unspecified PDB 2IFO . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1IFD _pdbx_database_status.recvd_initial_deposition_date 1992-02-16 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site ? _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? # _audit_author.name 'Marvin, D.A.' _audit_author.pdbx_ordinal 1 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Model-building studies of Inovirus: genetic variations on a geometric theme.' Int.J.Biol.Macromol. 12 125 138 1990 IJBMDR UK 0141-8130 0708 ? 2078529 '10.1016/0141-8130(90)90064-H' 1 'Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions' Int.J.Biol.Macromol. 11 159 ? 1989 IJBMDR UK 0141-8130 0708 ? ? ? 2 'Filamentous Bacterial Viruses' J.Biosci. 8 799 ? 1985 JOBSDN II 0250-4774 1073 ? ? ? 3 'X-Ray Fiber Diffraction' 'Structural Molecular Biology' ? 3 ? 1982 ? ? 0-306-40982-8 2027 'Plenum Press, New York' ? ? 4 'Structure of the Protein and DNA in Fd Filamentous Bacterial Virus' Nature 289 814 ? 1981 NATUAS UK 0028-0836 0006 ? ? ? 5 'Filamentous Bacterial Viruses Xii. Molecular Architecture of the Class I (Fd, If1, Ike) Virion' J.Mol.Biol. 88 581 ? 1974 JMOBAK UK 0022-2836 0070 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Marvin, D.A.' 1 1 'Marvin, D.A.' 2 2 'Marvin, D.A.' 3 3 'Marvin, D.A.' 4 3 'Nave, C.' 5 4 'Banner, D.W.' 6 4 'Nave, C.' 7 4 'Marvin, D.A.' 8 5 'Marvin, D.A.' 9 5 'Pigram, W.J.' 10 5 'Wiseman, R.L.' 11 5 'Wachtel, E.J.' 12 5 'Marvin, F.J.' 13 # loop_ _citation_editor.citation_id _citation_editor.name _citation_editor.ordinal 3 'Davies, D.B.' 1 3 'Saenger, W.' 2 3 'Danyluk, S.S.' 3 # _cell.entry_id 1IFD _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1IFD _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description INOVIRUS _entity.formula_weight 5244.000 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS _entity_poly.pdbx_seq_one_letter_code_can AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS _entity_poly.pdbx_strand_id A _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 ALA n 1 2 GLU n 1 3 GLY n 1 4 ASP n 1 5 ASP n 1 6 PRO n 1 7 ALA n 1 8 LYS n 1 9 ALA n 1 10 ALA n 1 11 PHE n 1 12 ASP n 1 13 SER n 1 14 LEU n 1 15 GLN n 1 16 ALA n 1 17 SER n 1 18 ALA n 1 19 THR n 1 20 GLU n 1 21 TYR n 1 22 ILE n 1 23 GLY n 1 24 TYR n 1 25 ALA n 1 26 TRP n 1 27 ALA n 1 28 MET n 1 29 VAL n 1 30 VAL n 1 31 VAL n 1 32 ILE n 1 33 VAL n 1 34 GLY n 1 35 ALA n 1 36 THR n 1 37 ILE n 1 38 GLY n 1 39 ILE n 1 40 LYS n 1 41 LEU n 1 42 PHE n 1 43 LYS n 1 44 LYS n 1 45 PHE n 1 46 THR n 1 47 SER n 1 48 LYS n 1 49 ALA n 1 50 SER n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus Inovirus _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species 'Enterobacteria phage M13' _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Enterobacteria phage fd' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10864 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name ? _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ? _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type BACTERIA _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name M13 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code COATB_BPFD _struct_ref.entity_id 1 _struct_ref.pdbx_db_accession P69539 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code MKKSLVLKASVAVATLVPMLSFAAEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1IFD _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 50 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P69539 _struct_ref_seq.db_align_beg 24 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 73 _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 50 # 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 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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 1IFD _exptl.method 'FIBER DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _refine.entry_id 1IFD _refine.ls_number_reflns_obs ? _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 ? _refine.ls_d_res_high 4.00 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ;THE MODEL OF THE VIRION HELIX ASYMMETRIC UNIT IS AN ALPHA-HELIX APPROXIMATION TO THE STRUCTURE, SO THE ENTIRE MODEL IS ONE STRETCH OF GENTLY-CURVED HELIX. COORDINATES ARE GIVEN FOR A SINGLE ASYMMETRIC UNIT OF THE COAT PROTEIN ASSEMBLY. THE COMPLETE PROTEIN ASSEMBLY CONTAINS SEVERAL THOUSAND ASYMMETRIC UNITS; THE EXACT NUMBER DEPENDS ON THE LENGTH OF THE DNA. THE PROTEIN ASSEMBLY FORMS A CYLINDRICAL SHELL SURROUNDING A DNA CORE. THE DNA IS ABOUT 12% BY WEIGHT OF THE FD VIRION, AND PROBABLY HAS NO WELL-DEFINED STRUCTURE OTHER THAN THAT IMPOSED BY ITS SINGLE-STRANDED CIRCULAR TOPOLOGY: TWO OPPOSITELY DIRECTED DNA CHAINS RUN ALONG THE LENGTH OF THE VIRION TO COMPLETE THE CIRCLE. THE DNA MAY BE A LEFT-HANDED HELIX (SEE JRNL REFERENCE). THE TWO ENDS OF THE VIRION ARE CAPPED BY A FEW COPIES OF MINOR COAT PROTEINS, WHOSE STRUCTURE IS NOT KNOWN. THESE PROTEINS INTERACT WITH THE ENDS OF THE MAJOR COAT PROTEIN ASSEMBLY. THE N-TERMINAL END OF INOVIRUS HAS AN OPEN CUP SHAPE, AND THE C-TERMINAL END IS THE COMPLEMENT OF THIS, A POINTED ARROWHEAD SHAPE (SEE REFERENCES 1 AND 2). THE TWO ENDS OF THE FD ASSEMBLY CAN BE GENERATED BY OPERATING REPEATEDLY (SAY 10 - 20 TIMES) ON THE HELIX UNIT CELL CONTENTS (THE GROUP OF 5 ASYMMETRIC UNITS) WITH THE HELIX PARAMETERS, GIVING TWO DIFFERENT ENDS CONNECTED BY A SHORT SHAFT. SINCE THE MAJOR COAT PROTEIN SUBUNITS AT THE ENDS HAVE FEWER NEIGHBORS THAN THOSE IN THE CENTER OF THE ASSEMBLY, THEIR CONFORMATIONS ARE LESS CONSTRAINED AND MAY BE MODIFIED BY INTERACTION WITH THE MINOR COAT PROTEINS. THE HELIX UNIT CELL PARAMETERS ARE AFFECTED BY EXPERIMENTAL CONDITIONS SUCH AS HYDRATION, PH AND TEMPERATURE. BECAUSE OF THE OVERLAPPING INTERDIGITATED NATURE OF THE ASSEMBLY, EVEN SMALL CHANGES IN THE UNIT CELL PARAMETERS ARE ACCOMPANIED BY CHANGES IN THE SHAPE OF THE ASYMMETRIC UNIT. THESE CHANGES DO NOT ALTER THE PATTERN OF SIDE CHAIN INTERLOCKING BETWEEN NEIGHBORING ASYMMETRIC UNITS, BUT THEY CAN ALTER LOCAL NON-BONDED CONTACTS BY SEVERAL TENTHS OF AN ANGSTROM. THE DEPOSITORS DEFINE A CANONICAL HELIX UNIT CELL WITH PARAMETERS T = -33.23 DEGREES, P = 16.0 ANGSTROMS AND GIVE THE ATOMIC COORDINATES FOR THE ASYMMETRIC UNIT IN THIS UNIT CELL. TO DETERMINE THE COORDINATES OF THE ASYMMETRIC UNIT IN A NEW UNIT CELL WITH SLIGHTLY DIFFERENT PARAMETERS (T', P'), CONVERT FROM CARTESIAN COORDINATES TO CYLINDRICAL-POLAR COORDINATES AND USE EQUATION 5 OF THE JRNL REFERENCE. AN EQUIVALENT ALTERNATIVE METHOD IS TO APPLY A VARIABLE MATRIX THAT IS A FUNCTION OF THE Z COORDINATE OF THE ATOMS. DEFINE A SLEW COEFFICIENT S=(T'-T)/P; FOR EXAMPLE, FOR FD AT PH 2, T'=-36.0 DEGREES DEGREES, P'=16.15 ANGSTROMS AND S=-0.173 DEGREE/ANGSTROM. THEN, TO GENERATE THE SLEWED COORDINATES, APPLY THE MATRIX AND VECTOR (RECALCULATED FOR EACH ATOM): | COS(S*Z) -SIN(S*Z) 0 | | 0 | | SIN(S*Z) COS(S*Z) 0 | + | 0 | | 0 0 1 | | (P'/P)*Z | SLEWING THE COORDINATES IN THIS WAY GIVES RISE TO SMALL LOCAL DISTORTIONS IN COVALENT BOND LENGTHS AND BOND ANGLES, WHICH CAN BE CORRECTED BY A FEW CYCLES OF ENERGY MINIMIZATION. THE TEMPERATURE FACTOR WAS NOT REFINED AND IS GIVEN THE ARBITRARY VALUE OF 10. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'FIBER DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _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 'FIBER DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 370 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 370 _refine_hist.d_res_high 4.00 _refine_hist.d_res_low . # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function o_bond_d 0.004 ? ? ? 'FIBER DIFFRACTION' ? o_bond_d_na ? ? ? ? 'FIBER DIFFRACTION' ? o_bond_d_prot ? ? ? ? 'FIBER DIFFRACTION' ? o_angle_d ? ? ? ? 'FIBER DIFFRACTION' ? o_angle_d_na ? ? ? ? 'FIBER DIFFRACTION' ? o_angle_d_prot ? ? ? ? 'FIBER DIFFRACTION' ? o_angle_deg ? ? ? ? 'FIBER DIFFRACTION' ? o_angle_deg_na ? ? ? ? 'FIBER DIFFRACTION' ? o_angle_deg_prot ? ? ? ? 'FIBER DIFFRACTION' ? o_dihedral_angle_d ? ? ? ? 'FIBER DIFFRACTION' ? o_dihedral_angle_d_na ? ? ? ? 'FIBER DIFFRACTION' ? o_dihedral_angle_d_prot ? ? ? ? 'FIBER DIFFRACTION' ? o_improper_angle_d ? ? ? ? 'FIBER DIFFRACTION' ? o_improper_angle_d_na ? ? ? ? 'FIBER DIFFRACTION' ? o_improper_angle_d_prot ? ? ? ? 'FIBER DIFFRACTION' ? o_mcbond_it ? ? ? ? 'FIBER DIFFRACTION' ? o_mcangle_it ? ? ? ? 'FIBER DIFFRACTION' ? o_scbond_it ? ? ? ? 'FIBER DIFFRACTION' ? o_scangle_it ? ? ? ? 'FIBER DIFFRACTION' ? # _struct.entry_id 1IFD _struct.title 'MODEL-BUILDING STUDIES OF INOVIRUS: GENETIC VARIATIONS ON A GEOMETRIC THEME' _struct.pdbx_descriptor 'INOVIRUS (FILAMENTOUS BACTERIOPHAGE) STRAIN FD MAJOR COAT PROTEIN ASSEMBLY (FIBER DIFFRACTION)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1IFD _struct_keywords.pdbx_keywords VIRUS _struct_keywords.text 'VIRUS, Helical virus' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag Y _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id A _struct_conf.beg_label_comp_id ALA _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 SER _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 50 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ALA _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 1 _struct_conf.end_auth_comp_id SER _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 50 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 50 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _database_PDB_matrix.entry_id 1IFD _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1IFD _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _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] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # 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 ALA 1 1 1 ALA ALA A . n A 1 2 GLU 2 2 2 GLU GLU A . n A 1 3 GLY 3 3 3 GLY GLY A . n A 1 4 ASP 4 4 4 ASP ASP A . n A 1 5 ASP 5 5 5 ASP ASP A . n A 1 6 PRO 6 6 6 PRO PRO A . n A 1 7 ALA 7 7 7 ALA ALA A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 ALA 9 9 9 ALA ALA A . n A 1 10 ALA 10 10 10 ALA ALA A . n A 1 11 PHE 11 11 11 PHE PHE A . n A 1 12 ASP 12 12 12 ASP ASP A . n A 1 13 SER 13 13 13 SER SER A . n A 1 14 LEU 14 14 14 LEU LEU A . n A 1 15 GLN 15 15 15 GLN GLN A . n A 1 16 ALA 16 16 16 ALA ALA A . n A 1 17 SER 17 17 17 SER SER A . n A 1 18 ALA 18 18 18 ALA ALA A . n A 1 19 THR 19 19 19 THR THR A . n A 1 20 GLU 20 20 20 GLU GLU A . n A 1 21 TYR 21 21 21 TYR TYR A . n A 1 22 ILE 22 22 22 ILE ILE A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 TYR 24 24 24 TYR TYR A . n A 1 25 ALA 25 25 25 ALA ALA A . n A 1 26 TRP 26 26 26 TRP TRP A . n A 1 27 ALA 27 27 27 ALA ALA A . n A 1 28 MET 28 28 28 MET MET A . n A 1 29 VAL 29 29 29 VAL VAL A . n A 1 30 VAL 30 30 30 VAL VAL A . n A 1 31 VAL 31 31 31 VAL VAL A . n A 1 32 ILE 32 32 32 ILE ILE A . n A 1 33 VAL 33 33 33 VAL VAL A . n A 1 34 GLY 34 34 34 GLY GLY A . n A 1 35 ALA 35 35 35 ALA ALA A . n A 1 36 THR 36 36 36 THR THR A . n A 1 37 ILE 37 37 37 ILE ILE A . n A 1 38 GLY 38 38 38 GLY GLY A . n A 1 39 ILE 39 39 39 ILE ILE A . n A 1 40 LYS 40 40 40 LYS LYS A . n A 1 41 LEU 41 41 41 LEU LEU A . n A 1 42 PHE 42 42 42 PHE PHE A . n A 1 43 LYS 43 43 43 LYS LYS A . n A 1 44 LYS 44 44 44 LYS LYS A . n A 1 45 PHE 45 45 45 PHE PHE A . n A 1 46 THR 46 46 46 THR THR A . n A 1 47 SER 47 47 47 SER SER A . n A 1 48 LYS 48 48 48 LYS LYS A . n A 1 49 ALA 49 49 49 ALA ALA A . n A 1 50 SER 50 50 50 SER SER A . n # 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 'representative helical assembly' ? helical 55 2 'helical asymmetric unit' ? monomeric 1 3 'helical asymmetric unit, std helical frame' ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 '(1-55)' A 2 1 A 3 H A # 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] H 'transform to helical frame' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 1 'helical symmetry operation' ? ? -0.97092575 -0.23938084 0.00000000 0.00000 0.23938084 -0.97092575 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -80.00000 2 'helical symmetry operation' ? ? -0.52769727 0.84943251 0.00000000 0.00000 -0.84943251 -0.52769727 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -80.00000 3 'helical symmetry operation' ? ? 0.64479090 0.76435901 0.00000000 0.00000 -0.76435901 0.64479090 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -80.00000 4 'helical symmetry operation' ? ? 0.92619996 -0.37703267 0.00000000 0.00000 0.37703267 0.92619996 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -80.00000 5 'helical symmetry operation' ? ? -0.07236785 -0.99737801 0.00000000 0.00000 0.99737801 -0.07236785 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -80.00000 6 'helical symmetry operation' ? ? -0.68097653 -0.73230524 0.00000000 0.00000 0.73230524 -0.68097653 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -64.00000 7 'helical symmetry operation' ? ? -0.90689699 0.42135241 0.00000000 0.00000 -0.42135241 -0.90689699 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -64.00000 8 'helical symmetry operation' ? ? 0.12048337 0.99271535 0.00000000 0.00000 -0.99271535 0.12048337 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -64.00000 9 'helical symmetry operation' ? ? 0.98135981 0.19217942 0.00000000 0.00000 -0.19217942 0.98135981 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -64.00000 10 'helical symmetry operation' ? ? 0.48603035 -0.87394193 0.00000000 0.00000 0.87394193 0.48603035 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -64.00000 11 'helical symmetry operation' ? ? -0.16831734 -0.98573286 0.00000000 0.00000 0.98573286 -0.16831734 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -48.00000 12 'helical symmetry operation' ? ? -0.98950058 -0.14452890 0.00000000 0.00000 0.14452890 -0.98950058 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -48.00000 13 'helical symmetry operation' ? ? -0.44322765 0.89640909 0.00000000 0.00000 -0.89640909 -0.44322765 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -48.00000 14 'helical symmetry operation' ? ? 0.71557083 0.69854019 0.00000000 0.00000 -0.69854019 0.71557083 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -48.00000 15 'helical symmetry operation' ? ? 0.88547474 -0.46468751 0.00000000 0.00000 0.46468751 0.88547474 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -48.00000 16 'helical symmetry operation' ? ? 0.39938920 -0.91678147 0.00000000 0.00000 0.91678147 0.39938920 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -32.00000 17 'helical symmetry operation' ? ? -0.74849294 -0.66314276 0.00000000 0.00000 0.66314276 -0.74849294 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -32.00000 18 'helical symmetry operation' ? ? -0.86198328 0.50693671 0.00000000 0.00000 -0.50693671 -0.86198328 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -32.00000 19 'helical symmetry operation' ? ? 0.21575798 0.97644687 0.00000000 0.00000 -0.97644687 0.21575798 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -32.00000 20 'helical symmetry operation' ? ? 0.99532904 0.09654065 0.00000000 0.00000 -0.09654065 0.99532904 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -32.00000 21 'helical symmetry operation' ? ? 0.83647750 -0.54800128 0.00000000 0.00000 0.54800128 0.83647750 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -16.00000 22 'helical symmetry operation' ? ? -0.26269442 -0.96487908 0.00000000 0.00000 0.96487908 -0.26269442 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -16.00000 23 'helical symmetry operation' ? ? -0.99883158 -0.04832679 0.00000000 0.00000 0.04832679 -0.99883158 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -16.00000 24 'helical symmetry operation' ? ? -0.35461744 0.93501148 0.00000000 0.00000 -0.93501148 -0.35461744 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -16.00000 25 'helical symmetry operation' ? ? 0.77966595 0.62619567 0.00000000 0.00000 -0.62619567 0.77966595 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -16.00000 26 'helical symmetry operation' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 27 'helical symmetry operation' ? ? 0.30901699 -0.95105652 0.00000000 0.00000 0.95105652 0.30901699 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 28 'helical symmetry operation' ? ? -0.80901699 -0.58778525 0.00000000 0.00000 0.58778525 -0.80901699 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 29 'helical symmetry operation' ? ? -0.80901699 0.58778525 0.00000000 0.00000 -0.58778525 -0.80901699 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 30 'helical symmetry operation' ? ? 0.30901699 0.95105652 0.00000000 0.00000 -0.95105652 0.30901699 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 31 'helical symmetry operation' ? ? 0.83647750 0.54800128 0.00000000 0.00000 -0.54800128 0.83647750 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 16.00000 32 'helical symmetry operation' ? ? 0.77966595 -0.62619567 0.00000000 0.00000 0.62619567 0.77966595 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 16.00000 33 'helical symmetry operation' ? ? -0.35461744 -0.93501148 0.00000000 0.00000 0.93501148 -0.35461744 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 16.00000 34 'helical symmetry operation' ? ? -0.99883158 0.04832679 0.00000000 0.00000 -0.04832679 -0.99883158 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 16.00000 35 'helical symmetry operation' ? ? -0.26269442 0.96487908 0.00000000 0.00000 -0.96487908 -0.26269442 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 16.00000 36 'helical symmetry operation' ? ? 0.39938920 0.91678147 0.00000000 0.00000 -0.91678147 0.39938920 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 32.00000 37 'helical symmetry operation' ? ? 0.99532904 -0.09654065 0.00000000 0.00000 0.09654065 0.99532904 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 32.00000 38 'helical symmetry operation' ? ? 0.21575798 -0.97644687 0.00000000 0.00000 0.97644687 0.21575798 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 32.00000 39 'helical symmetry operation' ? ? -0.86198328 -0.50693671 0.00000000 0.00000 0.50693671 -0.86198328 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 32.00000 40 'helical symmetry operation' ? ? -0.74849294 0.66314276 0.00000000 0.00000 -0.66314276 -0.74849294 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 32.00000 41 'helical symmetry operation' ? ? -0.16831734 0.98573286 0.00000000 0.00000 -0.98573286 -0.16831734 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 48.00000 42 'helical symmetry operation' ? ? 0.88547474 0.46468751 0.00000000 0.00000 -0.46468751 0.88547474 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 48.00000 43 'helical symmetry operation' ? ? 0.71557083 -0.69854019 0.00000000 0.00000 0.69854019 0.71557083 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 48.00000 44 'helical symmetry operation' ? ? -0.44322765 -0.89640909 0.00000000 0.00000 0.89640909 -0.44322765 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 48.00000 45 'helical symmetry operation' ? ? -0.98950058 0.14452890 0.00000000 0.00000 -0.14452890 -0.98950058 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 48.00000 46 'helical symmetry operation' ? ? -0.68097653 0.73230524 0.00000000 0.00000 -0.73230524 -0.68097653 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 64.00000 47 'helical symmetry operation' ? ? 0.48603035 0.87394193 0.00000000 0.00000 -0.87394193 0.48603035 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 64.00000 48 'helical symmetry operation' ? ? 0.98135981 -0.19217942 0.00000000 0.00000 0.19217942 0.98135981 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 64.00000 49 'helical symmetry operation' ? ? 0.12048337 -0.99271535 0.00000000 0.00000 0.99271535 0.12048337 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 64.00000 50 'helical symmetry operation' ? ? -0.90689699 -0.42135241 0.00000000 0.00000 0.42135241 -0.90689699 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 64.00000 51 'helical symmetry operation' ? ? -0.97092575 0.23938084 0.00000000 0.00000 -0.23938084 -0.97092575 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 80.00000 52 'helical symmetry operation' ? ? -0.07236785 0.99737801 0.00000000 0.00000 -0.99737801 -0.07236785 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 80.00000 53 'helical symmetry operation' ? ? 0.92619996 0.37703267 0.00000000 0.00000 -0.37703267 0.92619996 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 80.00000 54 'helical symmetry operation' ? ? 0.64479090 -0.76435901 0.00000000 0.00000 0.76435901 0.64479090 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 80.00000 55 'helical symmetry operation' ? ? -0.52769727 -0.84943251 0.00000000 0.00000 0.84943251 -0.52769727 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 80.00000 # _pdbx_helical_symmetry.entry_id 1IFD _pdbx_helical_symmetry.number_of_operations 55 _pdbx_helical_symmetry.rotation_per_n_subunits -33.230000 _pdbx_helical_symmetry.rise_per_n_subunits 16.000000 _pdbx_helical_symmetry.n_subunits_divisor 1 _pdbx_helical_symmetry.dyad_axis no _pdbx_helical_symmetry.circular_symmetry 5 # 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 1994-07-31 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' # _software.name EREF _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _pdbx_entry_details.entry_id 1IFD _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ;INOVIRUS STRAIN FD WAS GROWN IN ESCHERICHIA COLI. THERE ARE TWO SYMMETRY CLASSES OF INOVIRUS. CLASS I INCLUDES STRAINS FD, IF1 AND IKE. CLASS II INCLUDES STRAINS PF1 AND XF. STRAIN FD BELONGS TO THE FF GROUP WITHIN CLASS I. THE MEMBERS OF THE FF GROUP HAVE VIRTUALLY IDENTICAL COAT PROTEIN SEQUENCES AND ONLY SLIGHTLY DIFFERENT GENOME SEQUENCES. OTHER COMMONLY STUDIED FF STRAINS ARE F1, WHICH HAS THE SAME COAT PROTEIN SEQUENCE AS FD; AND M13, WHICH HAS AN ASP TO ASN EXCHANGE AT POSITION 12. THE COORDINATES OF THE M13 MODEL CAN BE DERIVED BY SUBSTITUTING ASN 12 FOR ASP 12 IN THE FD MODEL. MEMBERS OF THE FF GROUP GROW IN ESCHERICHIA COLI BACTERIA THAT CARRY THE F-FACTOR GENES. SOME OF THESE GENES ARE REQUIRED TO GENERATE THE F-PILI, WHICH ARE PROTEIN APPENDAGES THAT PROTRUDE FROM THE SURFACE OF THE BACTERIA AND ARE NECESSARY FOR ADSORPTION OF FD AS THE FIRST STEP IN INFECTION AND GROWTH. ; _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 NE1 _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 TRP _pdbx_validate_rmsd_bond.auth_seq_id_1 26 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 CE2 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 TRP _pdbx_validate_rmsd_bond.auth_seq_id_2 26 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.278 _pdbx_validate_rmsd_bond.bond_target_value 1.371 _pdbx_validate_rmsd_bond.bond_deviation -0.093 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.013 _pdbx_validate_rmsd_bond.linker_flag N #