data_1D5C # _entry.id 1D5C # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.286 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1D5C RCSB RCSB009802 WWPDB D_1000009802 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1D5C _pdbx_database_status.recvd_initial_deposition_date 1999-10-06 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Chattopadhyay, D.' 1 'Langsley, G.' 2 'Carson, M.' 3 'Recacha, R.' 4 'DeLucas, L.' 5 'Smith, C.' 6 # _citation.id primary _citation.title 'Structure of the nucleotide-binding domain of Plasmodium falciparum rab6 in the GDP-bound form.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 56 _citation.page_first 937 _citation.page_last 944 _citation.year 2000 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10944329 _citation.pdbx_database_id_DOI 10.1107/S0907444900007575 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Chattopadhyay, D.' 1 primary 'Langsley, G.' 2 primary 'Carson, M.' 3 primary 'Recacha, R.' 4 primary 'DeLucas, L.' 5 primary 'Smith, C.' 6 # _cell.entry_id 1D5C _cell.length_a 81.200 _cell.length_b 81.200 _cell.length_c 90.840 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 1D5C _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'RAB6 GTPASE' 18737.814 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn "GUANOSINE-5'-DIPHOSPHATE" 443.201 1 ? ? ? ? 4 water nat water 18.015 63 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;KYKLVFLGEQAVGKTSIITRF(MSE)YDTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAA AIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEG(MSE)QKAQEYNT(MSE)FHETSAKAG HNIKVLFKKTASKL ; _entity_poly.pdbx_seq_one_letter_code_can ;KYKLVFLGEQAVGKTSIITRFMYDTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVV YDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKTAS KL ; _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 LYS n 1 2 TYR n 1 3 LYS n 1 4 LEU n 1 5 VAL n 1 6 PHE n 1 7 LEU n 1 8 GLY n 1 9 GLU n 1 10 GLN n 1 11 ALA n 1 12 VAL n 1 13 GLY n 1 14 LYS n 1 15 THR n 1 16 SER n 1 17 ILE n 1 18 ILE n 1 19 THR n 1 20 ARG n 1 21 PHE n 1 22 MSE n 1 23 TYR n 1 24 ASP n 1 25 THR n 1 26 PHE n 1 27 ASP n 1 28 ASN n 1 29 ASN n 1 30 TYR n 1 31 GLN n 1 32 SER n 1 33 THR n 1 34 ILE n 1 35 GLY n 1 36 ILE n 1 37 ASP n 1 38 PHE n 1 39 LEU n 1 40 SER n 1 41 LYS n 1 42 THR n 1 43 LEU n 1 44 TYR n 1 45 LEU n 1 46 ASP n 1 47 GLU n 1 48 GLY n 1 49 PRO n 1 50 VAL n 1 51 ARG n 1 52 LEU n 1 53 GLN n 1 54 LEU n 1 55 TRP n 1 56 ASP n 1 57 THR n 1 58 ALA n 1 59 GLY n 1 60 GLN n 1 61 GLU n 1 62 ARG n 1 63 PHE n 1 64 ARG n 1 65 SER n 1 66 LEU n 1 67 ILE n 1 68 PRO n 1 69 SER n 1 70 TYR n 1 71 ILE n 1 72 ARG n 1 73 ASP n 1 74 SER n 1 75 ALA n 1 76 ALA n 1 77 ALA n 1 78 ILE n 1 79 VAL n 1 80 VAL n 1 81 TYR n 1 82 ASP n 1 83 ILE n 1 84 THR n 1 85 ASN n 1 86 ARG n 1 87 GLN n 1 88 SER n 1 89 PHE n 1 90 GLU n 1 91 ASN n 1 92 THR n 1 93 THR n 1 94 LYS n 1 95 TRP n 1 96 ILE n 1 97 GLN n 1 98 ASP n 1 99 ILE n 1 100 LEU n 1 101 ASN n 1 102 GLU n 1 103 ARG n 1 104 GLY n 1 105 LYS n 1 106 ASP n 1 107 VAL n 1 108 ILE n 1 109 ILE n 1 110 ALA n 1 111 LEU n 1 112 VAL n 1 113 GLY n 1 114 ASN n 1 115 LYS n 1 116 THR n 1 117 ASP n 1 118 LEU n 1 119 GLY n 1 120 ASP n 1 121 LEU n 1 122 ARG n 1 123 LYS n 1 124 VAL n 1 125 THR n 1 126 TYR n 1 127 GLU n 1 128 GLU n 1 129 GLY n 1 130 MSE n 1 131 GLN n 1 132 LYS n 1 133 ALA n 1 134 GLN n 1 135 GLU n 1 136 TYR n 1 137 ASN n 1 138 THR n 1 139 MSE n 1 140 PHE n 1 141 HIS n 1 142 GLU n 1 143 THR n 1 144 SER n 1 145 ALA n 1 146 LYS n 1 147 ALA n 1 148 GLY n 1 149 HIS n 1 150 ASN n 1 151 ILE n 1 152 LYS n 1 153 VAL n 1 154 LEU n 1 155 PHE n 1 156 LYS n 1 157 LYS n 1 158 THR n 1 159 ALA n 1 160 SER n 1 161 LYS n 1 162 LEU 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 'malaria parasite P. falciparum' _entity_src_gen.gene_src_genus Plasmodium _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 'Plasmodium falciparum' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 5833 _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 562 _entity_src_gen.host_org_genus Escherichia _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 ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PET21 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q26000_PLAFA _struct_ref.entity_id 1 _struct_ref.pdbx_db_accession Q26000 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1D5C _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 162 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q26000 _struct_ref_seq.db_align_beg 11 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 172 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 11 _struct_ref_seq.pdbx_auth_seq_align_end 172 # 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 1D5C MSE A 22 ? UNP Q26000 MET 32 'MODIFIED RESIDUE' 32 1 1 1D5C MSE A 130 ? UNP Q26000 MET 140 'MODIFIED RESIDUE' 140 2 1 1D5C MSE A 139 ? UNP Q26000 MET 149 'MODIFIED RESIDUE' 149 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 GDP 'RNA linking' n "GUANOSINE-5'-DIPHOSPHATE" ? 'C10 H15 N5 O11 P2' 443.201 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 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 1D5C _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.9 _exptl_crystal.density_percent_sol 68.0 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details 'sodium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K' _exptl_crystal_grow.pdbx_pH_range . # _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 1999-02-25 _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 MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9789 1.0 2 0.9770 1.0 3 0.9791 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type APS _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9789, 0.9770, 0.9791' # _reflns.entry_id 1D5C _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 2.2 _reflns.number_obs 15968 _reflns.number_all 15971 _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs 0.087 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 25.4 _reflns.B_iso_Wilson_estimate 20.0 _reflns.pdbx_redundancy 18.4 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.3 _reflns_shell.d_res_low 2.4 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.28 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 12.6 _reflns_shell.pdbx_redundancy 18.7 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1560 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1D5C _refine.ls_number_reflns_obs 13776 _refine.ls_number_reflns_all 13831 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_data_cutoff_high_absF 1501218.10 _refine.pdbx_data_cutoff_low_absF 0.00 _refine.ls_d_res_low 9.94 _refine.ls_d_res_high 2.30 _refine.ls_percent_reflns_obs 99.6 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.214 _refine.ls_R_factor_R_free 0.246 _refine.ls_R_factor_R_free_error 0.007 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.1 _refine.ls_number_reflns_R_free 1391 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 34.3 _refine.aniso_B[1][1] 0.00 _refine.aniso_B[2][2] 0.00 _refine.aniso_B[3][3] 0.00 _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 'FLAT MODEL' _refine.solvent_model_param_ksol 0.371 _refine.solvent_model_param_bsol 34.4068 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'F48 has been fixed because it lies on a two fold symmetry element.' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values MLF _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF 1501218.10 _refine.B_iso_min ? _refine.B_iso_max ? _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.overall_SU_R_Cruickshank_DPI ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1D5C _refine_analyze.Luzzati_coordinate_error_obs 0.31 _refine_analyze.Luzzati_sigma_a_obs 0.22 _refine_analyze.Luzzati_d_res_low_obs 10.00 _refine_analyze.Luzzati_coordinate_error_free 0.34 _refine_analyze.Luzzati_sigma_a_free 0.24 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1311 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 29 _refine_hist.number_atoms_solvent 63 _refine_hist.number_atoms_total 1403 _refine_hist.d_res_high 2.30 _refine_hist.d_res_low 9.94 # 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 c_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.2 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 23.3 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.63 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 3.44 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 3.51 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 1.82 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 2.84 2.50 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.30 _refine_ls_shell.d_res_low 2.44 _refine_ls_shell.number_reflns_R_work 2022 _refine_ls_shell.R_factor_R_work 0.25 _refine_ls_shell.percent_reflns_obs 99.8 _refine_ls_shell.R_factor_R_free 0.266 _refine_ls_shell.R_factor_R_free_error 0.017 _refine_ls_shell.percent_reflns_R_free 10.4 _refine_ls_shell.number_reflns_R_free 234 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 ION.PARAM ? 'X-RAY DIFFRACTION' 3 GDP_F.PARAM ? 'X-RAY DIFFRACTION' 4 WATER_REP.PARA ? 'X-RAY DIFFRACTION' # _struct.entry_id 1D5C _struct.title 'CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM RAB6 COMPLEXED WITH GDP' _struct.pdbx_descriptor 'RAB6 GTPASE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D5C _struct_keywords.pdbx_keywords ENDOCYTOSIS/EXOCYTOSIS _struct_keywords.text 'G-PROTEIN, GTPASE, RAB, RAB6, VESICULAR TRAFFICKING, ENDOCYTOSIS-EXOCYTOSIS COMPLEX' # 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 ? D N N 4 ? # _struct_biol.id 1 _struct_biol.details ? _struct_biol.pdbx_parent_biol_id ? # 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 GLY A 13 ? ASP A 24 ? GLY A 23 ASP A 34 1 ? 12 HELX_P HELX_P2 2 GLN A 60 ? SER A 65 ? GLN A 70 SER A 75 5 ? 6 HELX_P HELX_P3 3 LEU A 66 ? ARG A 72 ? LEU A 76 ARG A 82 1 ? 7 HELX_P HELX_P4 4 ASN A 85 ? ASN A 91 ? ASN A 95 ASN A 101 1 ? 7 HELX_P HELX_P5 5 ASN A 91 ? GLY A 104 ? ASN A 101 GLY A 114 1 ? 14 HELX_P HELX_P6 6 LYS A 115 ? GLY A 119 ? LYS A 125 GLY A 129 5 ? 5 HELX_P HELX_P7 7 LEU A 118 ? ARG A 122 ? LEU A 128 ARG A 132 5 ? 5 HELX_P HELX_P8 8 THR A 125 ? TYR A 136 ? THR A 135 TYR A 146 1 ? 12 HELX_P HELX_P9 9 ILE A 151 ? LYS A 161 ? ILE A 161 LYS A 171 1 ? 11 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A PHE 21 C ? ? ? 1_555 A MSE 22 N ? ? A PHE 31 A MSE 32 1_555 ? ? ? ? ? ? ? 1.329 ? covale2 covale ? ? A MSE 22 C ? ? ? 1_555 A TYR 23 N ? ? A MSE 32 A TYR 33 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? A GLY 129 C ? ? ? 1_555 A MSE 130 N ? ? A GLY 139 A MSE 140 1_555 ? ? ? ? ? ? ? 1.328 ? covale4 covale ? ? A MSE 130 C ? ? ? 1_555 A GLN 131 N ? ? A MSE 140 A GLN 141 1_555 ? ? ? ? ? ? ? 1.328 ? covale5 covale ? ? A THR 138 C ? ? ? 1_555 A MSE 139 N ? ? A THR 148 A MSE 149 1_555 ? ? ? ? ? ? ? 1.329 ? covale6 covale ? ? A MSE 139 C ? ? ? 1_555 A PHE 140 N ? ? A MSE 149 A PHE 150 1_555 ? ? ? ? ? ? ? 1.330 ? metalc1 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 300 A HOH 352 1_555 ? ? ? ? ? ? ? 2.137 ? metalc2 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 300 A HOH 353 1_555 ? ? ? ? ? ? ? 2.110 ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 300 A HOH 350 1_555 ? ? ? ? ? ? ? 2.042 ? metalc4 metalc ? ? B MG . MG ? ? ? 1_555 A THR 15 OG1 ? ? A MG 300 A THR 25 1_555 ? ? ? ? ? ? ? 2.179 ? metalc5 metalc ? ? B MG . MG ? ? ? 1_555 C GDP . O3B ? ? A MG 300 A GDP 201 1_555 ? ? ? ? ? ? ? 2.072 ? metalc6 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 300 A HOH 351 1_555 ? ? ? ? ? ? ? 2.001 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 6 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? parallel A 3 4 ? parallel A 4 5 ? parallel A 5 6 ? parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ASP A 37 ? LEU A 45 ? ASP A 47 LEU A 55 A 2 GLY A 48 ? ASP A 56 ? GLY A 58 ASP A 66 A 3 TYR A 2 ? LEU A 7 ? TYR A 12 LEU A 17 A 4 ALA A 76 ? ASP A 82 ? ALA A 86 ASP A 92 A 5 ILE A 108 ? ASN A 114 ? ILE A 118 ASN A 124 A 6 MSE A 139 ? GLU A 142 ? MSE A 149 GLU A 152 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O LEU A 45 ? O LEU A 55 N GLY A 48 ? N GLY A 58 A 2 3 N GLN A 53 ? N GLN A 63 O TYR A 2 ? O TYR A 12 A 3 4 N VAL A 5 ? N VAL A 15 O ALA A 76 ? O ALA A 86 A 4 5 N ALA A 77 ? N ALA A 87 O ILE A 108 ? O ILE A 118 A 5 6 N LEU A 111 ? N LEU A 121 O MSE A 139 ? O MSE A 149 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE MG A 300' AC2 Software ? ? ? ? 23 'BINDING SITE FOR RESIDUE GDP A 201' # 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 6 THR A 15 ? THR A 25 . ? 1_555 ? 2 AC1 6 GDP C . ? GDP A 201 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 350 . ? 1_555 ? 4 AC1 6 HOH D . ? HOH A 351 . ? 1_555 ? 5 AC1 6 HOH D . ? HOH A 352 . ? 1_555 ? 6 AC1 6 HOH D . ? HOH A 353 . ? 1_555 ? 7 AC2 23 GLN A 10 ? GLN A 20 . ? 1_555 ? 8 AC2 23 ALA A 11 ? ALA A 21 . ? 1_555 ? 9 AC2 23 VAL A 12 ? VAL A 22 . ? 1_555 ? 10 AC2 23 GLY A 13 ? GLY A 23 . ? 1_555 ? 11 AC2 23 LYS A 14 ? LYS A 24 . ? 1_555 ? 12 AC2 23 THR A 15 ? THR A 25 . ? 1_555 ? 13 AC2 23 SER A 16 ? SER A 26 . ? 1_555 ? 14 AC2 23 PHE A 26 ? PHE A 36 . ? 1_555 ? 15 AC2 23 TYR A 30 ? TYR A 40 . ? 1_555 ? 16 AC2 23 SER A 32 ? SER A 42 . ? 1_555 ? 17 AC2 23 ASN A 114 ? ASN A 124 . ? 1_555 ? 18 AC2 23 LYS A 115 ? LYS A 125 . ? 1_555 ? 19 AC2 23 ASP A 117 ? ASP A 127 . ? 1_555 ? 20 AC2 23 SER A 144 ? SER A 154 . ? 1_555 ? 21 AC2 23 ALA A 145 ? ALA A 155 . ? 1_555 ? 22 AC2 23 LYS A 146 ? LYS A 156 . ? 1_555 ? 23 AC2 23 MG B . ? MG A 300 . ? 1_555 ? 24 AC2 23 HOH D . ? HOH A 326 . ? 1_555 ? 25 AC2 23 HOH D . ? HOH A 332 . ? 1_555 ? 26 AC2 23 HOH D . ? HOH A 344 . ? 1_555 ? 27 AC2 23 HOH D . ? HOH A 350 . ? 1_555 ? 28 AC2 23 HOH D . ? HOH A 351 . ? 1_555 ? 29 AC2 23 HOH D . ? HOH A 352 . ? 1_555 ? # _database_PDB_matrix.entry_id 1D5C _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 1D5C _atom_sites.fract_transf_matrix[1][1] 0.012315 _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] 0.012315 _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] 0.011008 _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 MG N O P SE # 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 LYS 1 11 11 LYS LYS A . n A 1 2 TYR 2 12 12 TYR TYR A . n A 1 3 LYS 3 13 13 LYS LYS A . n A 1 4 LEU 4 14 14 LEU LEU A . n A 1 5 VAL 5 15 15 VAL VAL A . n A 1 6 PHE 6 16 16 PHE PHE A . n A 1 7 LEU 7 17 17 LEU LEU A . n A 1 8 GLY 8 18 18 GLY GLY A . n A 1 9 GLU 9 19 19 GLU GLU A . n A 1 10 GLN 10 20 20 GLN GLN A . n A 1 11 ALA 11 21 21 ALA ALA A . n A 1 12 VAL 12 22 22 VAL VAL A . n A 1 13 GLY 13 23 23 GLY GLY A . n A 1 14 LYS 14 24 24 LYS LYS A . n A 1 15 THR 15 25 25 THR THR A . n A 1 16 SER 16 26 26 SER SER A . n A 1 17 ILE 17 27 27 ILE ILE A . n A 1 18 ILE 18 28 28 ILE ILE A . n A 1 19 THR 19 29 29 THR THR A . n A 1 20 ARG 20 30 30 ARG ARG A . n A 1 21 PHE 21 31 31 PHE PHE A . n A 1 22 MSE 22 32 32 MSE MSE A . n A 1 23 TYR 23 33 33 TYR TYR A . n A 1 24 ASP 24 34 34 ASP ASP A . n A 1 25 THR 25 35 35 THR THR A . n A 1 26 PHE 26 36 36 PHE PHE A . n A 1 27 ASP 27 37 37 ASP ASP A . n A 1 28 ASN 28 38 38 ASN ASN A . n A 1 29 ASN 29 39 39 ASN ASN A . n A 1 30 TYR 30 40 40 TYR TYR A . n A 1 31 GLN 31 41 41 GLN GLN A . n A 1 32 SER 32 42 42 SER SER A . n A 1 33 THR 33 43 43 THR THR A . n A 1 34 ILE 34 44 44 ILE ILE A . n A 1 35 GLY 35 45 45 GLY GLY A . n A 1 36 ILE 36 46 46 ILE ILE A . n A 1 37 ASP 37 47 47 ASP ASP A . n A 1 38 PHE 38 48 48 PHE PHE A . n A 1 39 LEU 39 49 49 LEU LEU A . n A 1 40 SER 40 50 50 SER SER A . n A 1 41 LYS 41 51 51 LYS LYS A . n A 1 42 THR 42 52 52 THR THR A . n A 1 43 LEU 43 53 53 LEU LEU A . n A 1 44 TYR 44 54 54 TYR TYR A . n A 1 45 LEU 45 55 55 LEU LEU A . n A 1 46 ASP 46 56 56 ASP ASP A . n A 1 47 GLU 47 57 57 GLU GLU A . n A 1 48 GLY 48 58 58 GLY GLY A . n A 1 49 PRO 49 59 59 PRO PRO A . n A 1 50 VAL 50 60 60 VAL VAL A . n A 1 51 ARG 51 61 61 ARG ARG A . n A 1 52 LEU 52 62 62 LEU LEU A . n A 1 53 GLN 53 63 63 GLN GLN A . n A 1 54 LEU 54 64 64 LEU LEU A . n A 1 55 TRP 55 65 65 TRP TRP A . n A 1 56 ASP 56 66 66 ASP ASP A . n A 1 57 THR 57 67 67 THR THR A . n A 1 58 ALA 58 68 68 ALA ALA A . n A 1 59 GLY 59 69 69 GLY GLY A . n A 1 60 GLN 60 70 70 GLN GLN A . n A 1 61 GLU 61 71 71 GLU GLU A . n A 1 62 ARG 62 72 72 ARG ARG A . n A 1 63 PHE 63 73 73 PHE PHE A . n A 1 64 ARG 64 74 74 ARG ARG A . n A 1 65 SER 65 75 75 SER SER A . n A 1 66 LEU 66 76 76 LEU LEU A . n A 1 67 ILE 67 77 77 ILE ILE A . n A 1 68 PRO 68 78 78 PRO PRO A . n A 1 69 SER 69 79 79 SER SER A . n A 1 70 TYR 70 80 80 TYR TYR A . n A 1 71 ILE 71 81 81 ILE ILE A . n A 1 72 ARG 72 82 82 ARG ARG A . n A 1 73 ASP 73 83 83 ASP ASP A . n A 1 74 SER 74 84 84 SER SER A . n A 1 75 ALA 75 85 85 ALA ALA A . n A 1 76 ALA 76 86 86 ALA ALA A . n A 1 77 ALA 77 87 87 ALA ALA A . n A 1 78 ILE 78 88 88 ILE ILE A . n A 1 79 VAL 79 89 89 VAL VAL A . n A 1 80 VAL 80 90 90 VAL VAL A . n A 1 81 TYR 81 91 91 TYR TYR A . n A 1 82 ASP 82 92 92 ASP ASP A . n A 1 83 ILE 83 93 93 ILE ILE A . n A 1 84 THR 84 94 94 THR THR A . n A 1 85 ASN 85 95 95 ASN ASN A . n A 1 86 ARG 86 96 96 ARG ARG A . n A 1 87 GLN 87 97 97 GLN GLN A . n A 1 88 SER 88 98 98 SER SER A . n A 1 89 PHE 89 99 99 PHE PHE A . n A 1 90 GLU 90 100 100 GLU GLU A . n A 1 91 ASN 91 101 101 ASN ASN A . n A 1 92 THR 92 102 102 THR THR A . n A 1 93 THR 93 103 103 THR THR A . n A 1 94 LYS 94 104 104 LYS LYS A . n A 1 95 TRP 95 105 105 TRP TRP A . n A 1 96 ILE 96 106 106 ILE ILE A . n A 1 97 GLN 97 107 107 GLN GLN A . n A 1 98 ASP 98 108 108 ASP ASP A . n A 1 99 ILE 99 109 109 ILE ILE A . n A 1 100 LEU 100 110 110 LEU LEU A . n A 1 101 ASN 101 111 111 ASN ASN A . n A 1 102 GLU 102 112 112 GLU GLU A . n A 1 103 ARG 103 113 113 ARG ARG A . n A 1 104 GLY 104 114 114 GLY GLY A . n A 1 105 LYS 105 115 115 LYS LYS A . n A 1 106 ASP 106 116 116 ASP ASP A . n A 1 107 VAL 107 117 117 VAL VAL A . n A 1 108 ILE 108 118 118 ILE ILE A . n A 1 109 ILE 109 119 119 ILE ILE A . n A 1 110 ALA 110 120 120 ALA ALA A . n A 1 111 LEU 111 121 121 LEU LEU A . n A 1 112 VAL 112 122 122 VAL VAL A . n A 1 113 GLY 113 123 123 GLY GLY A . n A 1 114 ASN 114 124 124 ASN ASN A . n A 1 115 LYS 115 125 125 LYS LYS A . n A 1 116 THR 116 126 126 THR THR A . n A 1 117 ASP 117 127 127 ASP ASP A . n A 1 118 LEU 118 128 128 LEU LEU A . n A 1 119 GLY 119 129 129 GLY GLY A . n A 1 120 ASP 120 130 130 ASP ASP A . n A 1 121 LEU 121 131 131 LEU LEU A . n A 1 122 ARG 122 132 132 ARG ARG A . n A 1 123 LYS 123 133 133 LYS LYS A . n A 1 124 VAL 124 134 134 VAL VAL A . n A 1 125 THR 125 135 135 THR THR A . n A 1 126 TYR 126 136 136 TYR TYR A . n A 1 127 GLU 127 137 137 GLU GLU A . n A 1 128 GLU 128 138 138 GLU GLU A . n A 1 129 GLY 129 139 139 GLY GLY A . n A 1 130 MSE 130 140 140 MSE MSE A . n A 1 131 GLN 131 141 141 GLN GLN A . n A 1 132 LYS 132 142 142 LYS LYS A . n A 1 133 ALA 133 143 143 ALA ALA A . n A 1 134 GLN 134 144 144 GLN GLN A . n A 1 135 GLU 135 145 145 GLU GLU A . n A 1 136 TYR 136 146 146 TYR TYR A . n A 1 137 ASN 137 147 147 ASN ASN A . n A 1 138 THR 138 148 148 THR THR A . n A 1 139 MSE 139 149 149 MSE MSE A . n A 1 140 PHE 140 150 150 PHE PHE A . n A 1 141 HIS 141 151 151 HIS HIS A . n A 1 142 GLU 142 152 152 GLU GLU A . n A 1 143 THR 143 153 153 THR THR A . n A 1 144 SER 144 154 154 SER SER A . n A 1 145 ALA 145 155 155 ALA ALA A . n A 1 146 LYS 146 156 156 LYS LYS A . n A 1 147 ALA 147 157 157 ALA ALA A . n A 1 148 GLY 148 158 158 GLY GLY A . n A 1 149 HIS 149 159 159 HIS HIS A . n A 1 150 ASN 150 160 160 ASN ASN A . n A 1 151 ILE 151 161 161 ILE ILE A . n A 1 152 LYS 152 162 162 LYS LYS A . n A 1 153 VAL 153 163 163 VAL VAL A . n A 1 154 LEU 154 164 164 LEU LEU A . n A 1 155 PHE 155 165 165 PHE PHE A . n A 1 156 LYS 156 166 166 LYS LYS A . n A 1 157 LYS 157 167 167 LYS LYS A . n A 1 158 THR 158 168 168 THR THR A . n A 1 159 ALA 159 169 169 ALA ALA A . n A 1 160 SER 160 170 170 SER SER A . n A 1 161 LYS 161 171 171 LYS LYS A . n A 1 162 LEU 162 172 172 LEU LEU 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 MG 1 300 300 MG MG A . C 3 GDP 1 201 201 GDP GDP A . D 4 HOH 1 301 1 HOH HOH A . D 4 HOH 2 302 2 HOH HOH A . D 4 HOH 3 303 3 HOH HOH A . D 4 HOH 4 304 4 HOH HOH A . D 4 HOH 5 305 5 HOH HOH A . D 4 HOH 6 306 6 HOH HOH A . D 4 HOH 7 307 7 HOH HOH A . D 4 HOH 8 308 8 HOH HOH A . D 4 HOH 9 309 9 HOH HOH A . D 4 HOH 10 310 10 HOH HOH A . D 4 HOH 11 311 11 HOH HOH A . D 4 HOH 12 312 12 HOH HOH A . D 4 HOH 13 313 13 HOH HOH A . D 4 HOH 14 314 14 HOH HOH A . D 4 HOH 15 315 15 HOH HOH A . D 4 HOH 16 316 16 HOH HOH A . D 4 HOH 17 317 17 HOH HOH A . D 4 HOH 18 318 18 HOH HOH A . D 4 HOH 19 319 19 HOH HOH A . D 4 HOH 20 320 20 HOH HOH A . D 4 HOH 21 321 21 HOH HOH A . D 4 HOH 22 322 22 HOH HOH A . D 4 HOH 23 323 23 HOH HOH A . D 4 HOH 24 324 24 HOH HOH A . D 4 HOH 25 325 25 HOH HOH A . D 4 HOH 26 326 26 HOH HOH A . D 4 HOH 27 327 27 HOH HOH A . D 4 HOH 28 328 28 HOH HOH A . D 4 HOH 29 329 29 HOH HOH A . D 4 HOH 30 330 30 HOH HOH A . D 4 HOH 31 331 31 HOH HOH A . D 4 HOH 32 332 32 HOH HOH A . D 4 HOH 33 333 33 HOH HOH A . D 4 HOH 34 334 34 HOH HOH A . D 4 HOH 35 335 35 HOH HOH A . D 4 HOH 36 336 36 HOH HOH A . D 4 HOH 37 337 37 HOH HOH A . D 4 HOH 38 338 38 HOH HOH A . D 4 HOH 39 339 39 HOH HOH A . D 4 HOH 40 340 40 HOH HOH A . D 4 HOH 41 341 41 HOH HOH A . D 4 HOH 42 342 42 HOH HOH A . D 4 HOH 43 343 43 HOH HOH A . D 4 HOH 44 344 44 HOH HOH A . D 4 HOH 45 345 45 HOH HOH A . D 4 HOH 46 346 46 HOH HOH A . D 4 HOH 47 347 47 HOH HOH A . D 4 HOH 48 348 48 HOH HOH A . D 4 HOH 49 349 49 HOH HOH A . D 4 HOH 50 350 50 HOH HOH A . D 4 HOH 51 351 51 HOH HOH A . D 4 HOH 52 352 52 HOH HOH A . D 4 HOH 53 353 53 HOH HOH A . D 4 HOH 54 354 54 HOH HOH A . D 4 HOH 55 355 55 HOH HOH A . D 4 HOH 56 356 56 HOH HOH A . D 4 HOH 57 357 57 HOH HOH A . D 4 HOH 58 358 58 HOH HOH A . D 4 HOH 59 359 59 HOH HOH A . D 4 HOH 60 360 60 HOH HOH A . D 4 HOH 61 361 61 HOH HOH A . D 4 HOH 62 362 62 HOH HOH A . D 4 HOH 63 363 63 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 22 A MSE 32 ? MET SELENOMETHIONINE 2 A MSE 130 A MSE 140 ? MET SELENOMETHIONINE 3 A MSE 139 A MSE 149 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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,C,D # _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_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? D HOH . ? A HOH 352 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O ? D HOH . ? A HOH 353 ? 1_555 76.9 ? 2 O ? D HOH . ? A HOH 352 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O ? D HOH . ? A HOH 350 ? 1_555 159.6 ? 3 O ? D HOH . ? A HOH 353 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O ? D HOH . ? A HOH 350 ? 1_555 95.1 ? 4 O ? D HOH . ? A HOH 352 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 OG1 ? A THR 15 ? A THR 25 ? 1_555 78.9 ? 5 O ? D HOH . ? A HOH 353 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 OG1 ? A THR 15 ? A THR 25 ? 1_555 87.2 ? 6 O ? D HOH . ? A HOH 350 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 OG1 ? A THR 15 ? A THR 25 ? 1_555 82.1 ? 7 O ? D HOH . ? A HOH 352 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O3B ? C GDP . ? A GDP 201 ? 1_555 89.3 ? 8 O ? D HOH . ? A HOH 353 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O3B ? C GDP . ? A GDP 201 ? 1_555 164.3 ? 9 O ? D HOH . ? A HOH 350 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O3B ? C GDP . ? A GDP 201 ? 1_555 95.5 ? 10 OG1 ? A THR 15 ? A THR 25 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O3B ? C GDP . ? A GDP 201 ? 1_555 82.8 ? 11 O ? D HOH . ? A HOH 352 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O ? D HOH . ? A HOH 351 ? 1_555 90.1 ? 12 O ? D HOH . ? A HOH 353 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O ? D HOH . ? A HOH 351 ? 1_555 90.6 ? 13 O ? D HOH . ? A HOH 350 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O ? D HOH . ? A HOH 351 ? 1_555 109.0 ? 14 OG1 ? A THR 15 ? A THR 25 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O ? D HOH . ? A HOH 351 ? 1_555 168.9 ? 15 O3B ? C GDP . ? A GDP 201 ? 1_555 MG ? B MG . ? A MG 300 ? 1_555 O ? D HOH . ? A HOH 351 ? 1_555 96.9 ? # 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 2000-08-30 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-04 # _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' 3 4 'Structure model' Advisory 4 4 'Structure model' 'Refinement description' # 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 4 'Structure model' pdbx_unobs_or_zero_occ_atoms 2 4 'Structure model' pdbx_unobs_or_zero_occ_residues 3 4 'Structure model' software # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345 'data collection' . ? 1 d*TREK 'data reduction' . ? 2 SOLVE phasing . ? 3 CNS refinement 0.9 ? 4 d*TREK 'data scaling' . ? 5 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 SER A 42 ? ? -9.19 138.13 2 1 ASP A 56 ? ? -68.81 53.17 3 1 GLU A 57 ? ? -165.88 -18.25 4 1 ASP A 83 ? ? 57.77 16.36 5 1 ASP A 116 ? ? -85.01 42.99 6 1 LYS A 125 ? ? 76.74 45.06 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 "GUANOSINE-5'-DIPHOSPHATE" GDP 4 water HOH #