data_2CMP # _entry.id 2CMP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.308 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2CMP PDBE EBI-28703 WWPDB D_1290028703 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2CMP _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2006-05-11 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Benini, S.' 1 'Chechik, M.' 2 'Ortiz-Lombardia, M.' 3 'Polier, S.' 4 'Shevtsov, M.B.' 5 'DeLuchi, D.' 6 'Alonso, J.C.' 7 'Antson, A.A.' 8 # _citation.id primary _citation.title 'The 1.58 A Resolution Structure of the DNA-Binding Domain of Bacteriophage Sf6 Small Terminase Provides New Hints on DNA Binding' _citation.journal_abbrev 'Acta Crystallogr.,Sect.F' _citation.journal_volume 69 _citation.page_first 376 _citation.page_last ? _citation.year 2013 _citation.journal_id_ASTM ? _citation.country DK _citation.journal_id_ISSN 1744-3091 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23545641 _citation.pdbx_database_id_DOI 10.1107/S1744309113004399 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Benini, S.' 1 ? primary 'Chechik, M.' 2 ? primary 'Ortiz-Lombardia, M.' 3 ? primary 'Polier, S.' 4 ? primary 'Leech, A.' 5 ? primary 'Shevtsov, M.B.' 6 ? primary 'Alonso, J.C.' 7 ? # _cell.entry_id 2CMP _cell.length_a 57.286 _cell.length_b 57.286 _cell.length_c 57.286 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2CMP _symmetry.space_group_name_H-M 'P 21 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'TERMINASE SMALL SUBUNIT' 6959.960 1 ? ? 'DNA BINDING DOMAIN, RESIDUES 1-60' ? 2 water nat water 18.015 52 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name G1P # _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 GSHMKEPKLSPKQERFIEEYFINDMNATKAAIAAGYSKNSASAIGAENLQKPAIRARIDARLK _entity_poly.pdbx_seq_one_letter_code_can GSHMKEPKLSPKQERFIEEYFINDMNATKAAIAAGYSKNSASAIGAENLQKPAIRARIDARLK _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 GLY n 1 2 SER n 1 3 HIS n 1 4 MET n 1 5 LYS n 1 6 GLU n 1 7 PRO n 1 8 LYS n 1 9 LEU n 1 10 SER n 1 11 PRO n 1 12 LYS n 1 13 GLN n 1 14 GLU n 1 15 ARG n 1 16 PHE n 1 17 ILE n 1 18 GLU n 1 19 GLU n 1 20 TYR n 1 21 PHE n 1 22 ILE n 1 23 ASN n 1 24 ASP n 1 25 MET n 1 26 ASN n 1 27 ALA n 1 28 THR n 1 29 LYS n 1 30 ALA n 1 31 ALA n 1 32 ILE n 1 33 ALA n 1 34 ALA n 1 35 GLY n 1 36 TYR n 1 37 SER n 1 38 LYS n 1 39 ASN n 1 40 SER n 1 41 ALA n 1 42 SER n 1 43 ALA n 1 44 ILE n 1 45 GLY n 1 46 ALA n 1 47 GLU n 1 48 ASN n 1 49 LEU n 1 50 GLN n 1 51 LYS n 1 52 PRO n 1 53 ALA n 1 54 ILE n 1 55 ARG n 1 56 ALA n 1 57 ARG n 1 58 ILE n 1 59 ASP n 1 60 ALA n 1 61 ARG n 1 62 LEU n 1 63 LYS 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 ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'BACTERIOPHAGE SF6' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10773 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'ESCHERICHIA COLI' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 511693 _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 BL21 _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type PLASMID _entity_src_gen.pdbx_host_org_vector PET28A _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TERS_BPSF6 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P68928 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2CMP _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 63 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P68928 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 60 _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 60 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 2CMP GLY A 1 ? UNP P68928 ? ? 'expression tag' -2 1 1 2CMP SER A 2 ? UNP P68928 ? ? 'expression tag' -1 2 1 2CMP HIS A 3 ? UNP P68928 ? ? 'expression tag' 0 3 # 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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 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 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # _exptl.entry_id 2CMP _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.3 _exptl_crystal.density_percent_sol 45 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;HANGING DROP WITH 1 UL OF 17MG/ML PROTEIN IN 50MM HEPES PH7.5 10MM NACL MIXED WITH 1 UL OF 2.4 M NA MALONATE PH 7.0 AND EQUILIBRATED AGAINST 1ML OF 2.4 M NA MALONATE PH 7.0 AT 20C ; # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2005-12-01 _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 0.9765 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength 0.9765 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2CMP _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 23.400 _reflns.d_resolution_high 1.580 _reflns.number_obs 8787 _reflns.number_all ? _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs 0.04000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 38.7000 _reflns.B_iso_Wilson_estimate 35.10 _reflns.pdbx_redundancy 9.300 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.58 _reflns_shell.d_res_low 1.64 _reflns_shell.percent_possible_all 99.9 _reflns_shell.Rmerge_I_obs 0.56000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.200 _reflns_shell.pdbx_redundancy 5.90 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2CMP _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.ls_number_reflns_obs 8363 _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 40.52 _refine.ls_d_res_high 1.58 _refine.ls_percent_reflns_obs 99.9 _refine.ls_R_factor_obs 0.227 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.225 _refine.ls_R_factor_R_free 0.276 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.700 _refine.ls_number_reflns_R_free 408 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.956 _refine.correlation_coeff_Fo_to_Fc_free 0.928 _refine.B_iso_mean 46.07 _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 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _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. PROTEIN MODEL STARTS FROM RESIDUE LYS5' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _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 0.106 _refine.pdbx_overall_ESU_R_Free 0.112 _refine.overall_SU_ML 0.083 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 4.699 _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 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 435 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 52 _refine_hist.number_atoms_total 487 _refine_hist.d_res_high 1.58 _refine_hist.d_res_low 40.52 # 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 r_bond_refined_d 0.014 0.022 ? 489 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.488 1.989 ? 655 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.226 5.000 ? 62 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 36.439 23.333 ? 21 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 16.752 15.000 ? 98 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 16.898 15.000 ? 5 'X-RAY DIFFRACTION' ? r_chiral_restr 0.093 0.200 ? 71 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.020 ? 363 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.283 0.200 ? 261 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.310 0.200 ? 335 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.177 0.200 ? 32 '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 0.180 0.200 ? 31 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.247 0.200 ? 10 '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 1.551 2.000 ? 315 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 2.504 3.000 ? 492 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 3.792 6.000 ? 189 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 5.781 8.000 ? 162 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? '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_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.58 _refine_ls_shell.d_res_low 1.63 _refine_ls_shell.number_reflns_R_work 614 _refine_ls_shell.R_factor_R_work 0.2550 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.2980 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 34 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2CMP _struct.title 'crystal structure of the DNA binding domain of G1P SMALL TERMINASE SUBUNIT from bacteriophage SF6' _struct.pdbx_descriptor 'TERMINASE SMALL SUBUNIT' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2CMP _struct_keywords.pdbx_keywords 'VIRAL PROTEIN' _struct_keywords.text 'SF6, DNA PACKAGING, VIRAL 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 ? # _struct_biol.id 1 # 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 SER A 10 ? ASN A 23 ? SER A 7 ASN A 20 1 ? 14 HELX_P HELX_P2 2 ASN A 26 ? ALA A 34 ? ASN A 23 ALA A 31 1 ? 9 HELX_P HELX_P3 3 SER A 37 ? LYS A 51 ? SER A 34 LYS A 48 1 ? 15 HELX_P HELX_P4 4 LYS A 51 ? LYS A 63 ? LYS A 48 LYS A 60 1 ? 13 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _database_PDB_matrix.entry_id 2CMP _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 2CMP _atom_sites.fract_transf_matrix[1][1] 0.017456 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.017456 _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] 0.017456 _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 GLY 1 -2 ? ? ? A . n A 1 2 SER 2 -1 ? ? ? A . n A 1 3 HIS 3 0 ? ? ? A . n A 1 4 MET 4 1 ? ? ? A . n A 1 5 LYS 5 2 ? ? ? A . n A 1 6 GLU 6 3 ? ? ? A . n A 1 7 PRO 7 4 ? ? ? A . n A 1 8 LYS 8 5 5 LYS LYS A . n A 1 9 LEU 9 6 6 LEU LEU A . n A 1 10 SER 10 7 7 SER SER A . n A 1 11 PRO 11 8 8 PRO PRO A . n A 1 12 LYS 12 9 9 LYS LYS A . n A 1 13 GLN 13 10 10 GLN GLN A . n A 1 14 GLU 14 11 11 GLU GLU A . n A 1 15 ARG 15 12 12 ARG ARG A . n A 1 16 PHE 16 13 13 PHE PHE A . n A 1 17 ILE 17 14 14 ILE ILE A . n A 1 18 GLU 18 15 15 GLU GLU A . n A 1 19 GLU 19 16 16 GLU GLU A . n A 1 20 TYR 20 17 17 TYR TYR A . n A 1 21 PHE 21 18 18 PHE PHE A . n A 1 22 ILE 22 19 19 ILE ILE A . n A 1 23 ASN 23 20 20 ASN ASN A . n A 1 24 ASP 24 21 21 ASP ASP A . n A 1 25 MET 25 22 22 MET MET A . n A 1 26 ASN 26 23 23 ASN ASN A . n A 1 27 ALA 27 24 24 ALA ALA A . n A 1 28 THR 28 25 25 THR THR A . n A 1 29 LYS 29 26 26 LYS LYS A . n A 1 30 ALA 30 27 27 ALA ALA A . n A 1 31 ALA 31 28 28 ALA ALA A . n A 1 32 ILE 32 29 29 ILE ILE A . n A 1 33 ALA 33 30 30 ALA ALA A . n A 1 34 ALA 34 31 31 ALA ALA A . n A 1 35 GLY 35 32 32 GLY GLY A . n A 1 36 TYR 36 33 33 TYR TYR A . n A 1 37 SER 37 34 34 SER SER A . n A 1 38 LYS 38 35 35 LYS LYS A . n A 1 39 ASN 39 36 36 ASN ASN A . n A 1 40 SER 40 37 37 SER SER A . n A 1 41 ALA 41 38 38 ALA ALA A . n A 1 42 SER 42 39 39 SER SER A . n A 1 43 ALA 43 40 40 ALA ALA A . n A 1 44 ILE 44 41 41 ILE ILE A . n A 1 45 GLY 45 42 42 GLY GLY A . n A 1 46 ALA 46 43 43 ALA ALA A . n A 1 47 GLU 47 44 44 GLU GLU A . n A 1 48 ASN 48 45 45 ASN ASN A . n A 1 49 LEU 49 46 46 LEU LEU A . n A 1 50 GLN 50 47 47 GLN GLN A . n A 1 51 LYS 51 48 48 LYS LYS A . n A 1 52 PRO 52 49 49 PRO PRO A . n A 1 53 ALA 53 50 50 ALA ALA A . n A 1 54 ILE 54 51 51 ILE ILE A . n A 1 55 ARG 55 52 52 ARG ARG A . n A 1 56 ALA 56 53 53 ALA ALA A . n A 1 57 ARG 57 54 54 ARG ARG A . n A 1 58 ILE 58 55 55 ILE ILE A . n A 1 59 ASP 59 56 56 ASP ASP A . n A 1 60 ALA 60 57 57 ALA ALA A . n A 1 61 ARG 61 58 58 ARG ARG A . n A 1 62 LEU 62 59 59 LEU LEU A . n A 1 63 LYS 63 60 60 LYS LYS 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 HOH 1 2001 2001 HOH HOH A . B 2 HOH 2 2002 2002 HOH HOH A . B 2 HOH 3 2003 2003 HOH HOH A . B 2 HOH 4 2004 2004 HOH HOH A . B 2 HOH 5 2005 2005 HOH HOH A . B 2 HOH 6 2006 2006 HOH HOH A . B 2 HOH 7 2007 2007 HOH HOH A . B 2 HOH 8 2008 2008 HOH HOH A . B 2 HOH 9 2009 2009 HOH HOH A . B 2 HOH 10 2010 2010 HOH HOH A . B 2 HOH 11 2011 2011 HOH HOH A . B 2 HOH 12 2012 2012 HOH HOH A . B 2 HOH 13 2013 2013 HOH HOH A . B 2 HOH 14 2014 2014 HOH HOH A . B 2 HOH 15 2015 2015 HOH HOH A . B 2 HOH 16 2016 2016 HOH HOH A . B 2 HOH 17 2017 2017 HOH HOH A . B 2 HOH 18 2018 2018 HOH HOH A . B 2 HOH 19 2019 2019 HOH HOH A . B 2 HOH 20 2020 2020 HOH HOH A . B 2 HOH 21 2021 2021 HOH HOH A . B 2 HOH 22 2022 2022 HOH HOH A . B 2 HOH 23 2023 2023 HOH HOH A . B 2 HOH 24 2024 2024 HOH HOH A . B 2 HOH 25 2025 2025 HOH HOH A . B 2 HOH 26 2026 2026 HOH HOH A . B 2 HOH 27 2027 2027 HOH HOH A . B 2 HOH 28 2028 2028 HOH HOH A . B 2 HOH 29 2029 2029 HOH HOH A . B 2 HOH 30 2030 2030 HOH HOH A . B 2 HOH 31 2031 2031 HOH HOH A . B 2 HOH 32 2032 2032 HOH HOH A . B 2 HOH 33 2033 2033 HOH HOH A . B 2 HOH 34 2034 2034 HOH HOH A . B 2 HOH 35 2035 2035 HOH HOH A . B 2 HOH 36 2036 2036 HOH HOH A . B 2 HOH 37 2037 2037 HOH HOH A . B 2 HOH 38 2038 2038 HOH HOH A . B 2 HOH 39 2039 2039 HOH HOH A . B 2 HOH 40 2040 2040 HOH HOH A . B 2 HOH 41 2041 2041 HOH HOH A . B 2 HOH 42 2042 2042 HOH HOH A . B 2 HOH 43 2043 2043 HOH HOH A . B 2 HOH 44 2044 2044 HOH HOH A . B 2 HOH 45 2045 2045 HOH HOH A . B 2 HOH 46 2046 2046 HOH HOH A . B 2 HOH 47 2047 2047 HOH HOH A . B 2 HOH 48 2048 2048 HOH HOH A . B 2 HOH 49 2049 2049 HOH HOH A . B 2 HOH 50 2050 2050 HOH HOH A . B 2 HOH 51 2051 2051 HOH HOH A . B 2 HOH 52 2052 2052 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 2021 ? B HOH . 2 1 A HOH 2033 ? B HOH . 3 1 A HOH 2034 ? B HOH . 4 1 A HOH 2051 ? B HOH . # 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 2007-05-15 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2013-04-10 4 'Structure model' 1 3 2013-04-17 5 'Structure model' 1 4 2019-05-08 6 'Structure model' 1 5 2019-05-15 # _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' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 3 'Structure model' 'Derived calculations' 6 3 'Structure model' Other 7 3 'Structure model' 'Structure summary' 8 4 'Structure model' 'Database references' 9 4 'Structure model' 'Source and taxonomy' 10 5 'Structure model' Advisory 11 5 'Structure model' 'Data collection' 12 5 'Structure model' 'Experimental preparation' 13 5 'Structure model' Other 14 6 'Structure model' 'Data collection' 15 6 'Structure model' 'Experimental preparation' # 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 5 'Structure model' database_PDB_rev 2 5 'Structure model' database_PDB_rev_record 3 5 'Structure model' exptl_crystal_grow 4 5 'Structure model' pdbx_database_proc 5 5 'Structure model' pdbx_database_status 6 5 'Structure model' pdbx_validate_polymer_linkage 7 6 'Structure model' exptl_crystal_grow # 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 5 'Structure model' '_exptl_crystal_grow.method' 2 5 'Structure model' '_pdbx_database_status.recvd_author_approval' 3 5 'Structure model' '_pdbx_validate_polymer_linkage.dist' 4 5 'Structure model' '_pdbx_validate_polymer_linkage.label_alt_id_1' 5 5 'Structure model' '_pdbx_validate_polymer_linkage.label_alt_id_2' 6 6 'Structure model' '_exptl_crystal_grow.temp' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 22.3653 _pdbx_refine_tls.origin_y 8.6614 _pdbx_refine_tls.origin_z 34.0326 _pdbx_refine_tls.T[1][1] -0.0970 _pdbx_refine_tls.T[2][2] -0.1728 _pdbx_refine_tls.T[3][3] -0.2046 _pdbx_refine_tls.T[1][2] 0.0430 _pdbx_refine_tls.T[1][3] 0.0411 _pdbx_refine_tls.T[2][3] 0.0324 _pdbx_refine_tls.L[1][1] 4.9987 _pdbx_refine_tls.L[2][2] 8.4345 _pdbx_refine_tls.L[3][3] 3.6795 _pdbx_refine_tls.L[1][2] -2.0793 _pdbx_refine_tls.L[1][3] -1.1712 _pdbx_refine_tls.L[2][3] -1.0353 _pdbx_refine_tls.S[1][1] 0.1184 _pdbx_refine_tls.S[1][2] 0.2874 _pdbx_refine_tls.S[1][3] 0.3552 _pdbx_refine_tls.S[2][1] 0.5306 _pdbx_refine_tls.S[2][2] -0.2609 _pdbx_refine_tls.S[2][3] -0.2456 _pdbx_refine_tls.S[3][1] -0.3382 _pdbx_refine_tls.S[3][2] -0.3009 _pdbx_refine_tls.S[3][3] 0.1425 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 9 _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 60 _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0005 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 SHELX phasing . ? 4 # _pdbx_entry_details.entry_id 2CMP _pdbx_entry_details.compound_details 'ESSENTIAL FOR DNA MATURATION AND PACKAGING.' _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE FIRST THREE RESIDUES (GSH) IN THE SEQUENCE ARE THE REMNANT OF THE HISTIDINE TAG AFTER THROMBIN CLEAVAGE. ; # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE A ARG 54 ? ? CZ A ARG 54 ? ? NH1 A ARG 54 ? ? 123.48 120.30 3.18 0.50 N 2 1 NE A ARG 54 ? ? CZ A ARG 54 ? ? NH2 A ARG 54 ? ? 116.28 120.30 -4.02 0.50 N # loop_ _pdbx_validate_polymer_linkage.id _pdbx_validate_polymer_linkage.PDB_model_num _pdbx_validate_polymer_linkage.auth_atom_id_1 _pdbx_validate_polymer_linkage.auth_asym_id_1 _pdbx_validate_polymer_linkage.auth_comp_id_1 _pdbx_validate_polymer_linkage.auth_seq_id_1 _pdbx_validate_polymer_linkage.PDB_ins_code_1 _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.auth_atom_id_2 _pdbx_validate_polymer_linkage.auth_asym_id_2 _pdbx_validate_polymer_linkage.auth_comp_id_2 _pdbx_validate_polymer_linkage.auth_seq_id_2 _pdbx_validate_polymer_linkage.PDB_ins_code_2 _pdbx_validate_polymer_linkage.label_alt_id_2 _pdbx_validate_polymer_linkage.dist 1 1 C A LEU 6 ? B N A SER 7 ? B 4.73 2 1 C A LEU 6 ? A N A SER 7 ? A 5.25 # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 2002 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.81 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # 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 -2 ? A GLY 1 2 1 Y 1 A SER -1 ? A SER 2 3 1 Y 1 A HIS 0 ? A HIS 3 4 1 Y 1 A MET 1 ? A MET 4 5 1 Y 1 A LYS 2 ? A LYS 5 6 1 Y 1 A GLU 3 ? A GLU 6 7 1 Y 1 A PRO 4 ? A PRO 7 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #