data_3D6T # _entry.id 3D6T # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.290 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3D6T RCSB RCSB047664 WWPDB D_1000047664 # _pdbx_database_status.entry_id 3D6T _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-05-20 _pdbx_database_status.status_code REL _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 ? # _audit_author.name 'Deng, J.' _audit_author.pdbx_ordinal 1 _audit_author.identifier_ORCID ? # _citation.id primary _citation.title ;Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase ; _citation.journal_abbrev Proc.Natl.Acad.Sci.Usa _citation.journal_volume 105 _citation.page_first 1499 _citation.page_last 1504 _citation.year 2008 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18230735 _citation.pdbx_database_id_DOI 10.1073/pnas.0709098105 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Deng, J.' 1 primary 'Lewis, P.A.' 2 primary 'Greggio, E.' 3 primary 'Sluch, E.' 4 primary 'Beilina, A.' 5 primary 'Cookson, M.R.' 6 # _cell.entry_id 3D6T _cell.length_a 69.919 _cell.length_b 53.167 _cell.length_c 42.736 _cell.angle_alpha 90.00 _cell.angle_beta 112.76 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 3D6T _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _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 'Leucine-rich repeat serine/threonine-protein kinase 2' 19802.953 1 2.7.11.1 ? 'Miro domain' ? 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 6 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name Dardarin # _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 ;(MSE)KL(MSE)IVGNTGSGKTTLLQQL(MSE)KTKKSDLG(MSE)QSATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGR EEFYSTHPHF(MSE)TQRALYLAVYDLSKGQAEVDA(MSE)KPWLFNIKARASSSPVILVGTHLDVSDEKQRKAC(MSE) SKITKELLNKRGFPAIRDYHFVNATEESDALAKLRKTII ; _entity_poly.pdbx_seq_one_letter_code_can ;MKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQSATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRAL YLAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYHFVNATEES DALAKLRKTII ; _entity_poly.pdbx_strand_id B _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 MSE n 1 2 LYS n 1 3 LEU n 1 4 MSE n 1 5 ILE n 1 6 VAL n 1 7 GLY n 1 8 ASN n 1 9 THR n 1 10 GLY n 1 11 SER n 1 12 GLY n 1 13 LYS n 1 14 THR n 1 15 THR n 1 16 LEU n 1 17 LEU n 1 18 GLN n 1 19 GLN n 1 20 LEU n 1 21 MSE n 1 22 LYS n 1 23 THR n 1 24 LYS n 1 25 LYS n 1 26 SER n 1 27 ASP n 1 28 LEU n 1 29 GLY n 1 30 MSE n 1 31 GLN n 1 32 SER n 1 33 ALA n 1 34 THR n 1 35 VAL n 1 36 GLY n 1 37 ILE n 1 38 ASP n 1 39 VAL n 1 40 LYS n 1 41 ASP n 1 42 TRP n 1 43 PRO n 1 44 ILE n 1 45 GLN n 1 46 ILE n 1 47 ARG n 1 48 ASP n 1 49 LYS n 1 50 ARG n 1 51 LYS n 1 52 ARG n 1 53 ASP n 1 54 LEU n 1 55 VAL n 1 56 LEU n 1 57 ASN n 1 58 VAL n 1 59 TRP n 1 60 ASP n 1 61 PHE n 1 62 ALA n 1 63 GLY n 1 64 ARG n 1 65 GLU n 1 66 GLU n 1 67 PHE n 1 68 TYR n 1 69 SER n 1 70 THR n 1 71 HIS n 1 72 PRO n 1 73 HIS n 1 74 PHE n 1 75 MSE n 1 76 THR n 1 77 GLN n 1 78 ARG n 1 79 ALA n 1 80 LEU n 1 81 TYR n 1 82 LEU n 1 83 ALA n 1 84 VAL n 1 85 TYR n 1 86 ASP n 1 87 LEU n 1 88 SER n 1 89 LYS n 1 90 GLY n 1 91 GLN n 1 92 ALA n 1 93 GLU n 1 94 VAL n 1 95 ASP n 1 96 ALA n 1 97 MSE n 1 98 LYS n 1 99 PRO n 1 100 TRP n 1 101 LEU n 1 102 PHE n 1 103 ASN n 1 104 ILE n 1 105 LYS n 1 106 ALA n 1 107 ARG n 1 108 ALA n 1 109 SER n 1 110 SER n 1 111 SER n 1 112 PRO n 1 113 VAL n 1 114 ILE n 1 115 LEU n 1 116 VAL n 1 117 GLY n 1 118 THR n 1 119 HIS n 1 120 LEU n 1 121 ASP n 1 122 VAL n 1 123 SER n 1 124 ASP n 1 125 GLU n 1 126 LYS n 1 127 GLN n 1 128 ARG n 1 129 LYS n 1 130 ALA n 1 131 CYS n 1 132 MSE n 1 133 SER n 1 134 LYS n 1 135 ILE n 1 136 THR n 1 137 LYS n 1 138 GLU n 1 139 LEU n 1 140 LEU n 1 141 ASN n 1 142 LYS n 1 143 ARG n 1 144 GLY n 1 145 PHE n 1 146 PRO n 1 147 ALA n 1 148 ILE n 1 149 ARG n 1 150 ASP n 1 151 TYR n 1 152 HIS n 1 153 PHE n 1 154 VAL n 1 155 ASN n 1 156 ALA n 1 157 THR n 1 158 GLU n 1 159 GLU n 1 160 SER n 1 161 ASP n 1 162 ALA n 1 163 LEU n 1 164 ALA n 1 165 LYS n 1 166 LEU n 1 167 ARG n 1 168 LYS n 1 169 THR n 1 170 ILE n 1 171 ILE 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 Human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'LRRK2, PARK8' _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 469008 _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 BL21GOLDDE3 _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 ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PSKB3 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code LRRK2_HUMAN _struct_ref.pdbx_db_accession Q5S007 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;KLMIVGNTGSGKTTLLQQLMKTKKSDLGMQSATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALY LAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYHFVNATEESD ALAKLRKTII ; _struct_ref.pdbx_align_begin 1336 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3D6T _struct_ref_seq.pdbx_strand_id B _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 171 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q5S007 _struct_ref_seq.db_align_beg 1336 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 1505 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1336 _struct_ref_seq.pdbx_auth_seq_align_end 1505 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3D6T _struct_ref_seq_dif.mon_id MSE _struct_ref_seq_dif.pdbx_pdb_strand_id B _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q5S007 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'INITIATING METHIONINE' _struct_ref_seq_dif.pdbx_auth_seq_num 1335 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 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 3D6T _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.85 _exptl_crystal.density_percent_sol 33.49 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '30% PEG 4000, 100mM MgCl2, 0.1M Tris, 5mM GTP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K' # _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 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2007-06-21 _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 0.97926 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_wavelength 0.97926 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 3D6T _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 21.09 _reflns.d_resolution_high 2.43 _reflns.number_obs 5109 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 3D6T _refine.ls_number_reflns_obs 5109 _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 21.09 _refine.ls_d_res_high 2.43 _refine.ls_percent_reflns_obs 93.0 _refine.ls_R_factor_obs 0.216 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.211 _refine.ls_R_factor_R_free 0.307 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.500 _refine.ls_number_reflns_R_free 230 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.942 _refine.correlation_coeff_Fo_to_Fc_free 0.861 _refine.B_iso_mean 33.24 _refine.aniso_B[1][1] -0.08000 _refine.aniso_B[2][2] -0.48000 _refine.aniso_B[3][3] 0.59000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.04000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _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 ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.288 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 25.808 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _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 994 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 29 _refine_hist.number_atoms_solvent 6 _refine_hist.number_atoms_total 1029 _refine_hist.d_res_high 2.43 _refine_hist.d_res_low 21.09 # 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 0.023 0.022 ? 1023 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.342 1.995 ? 1383 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 8.302 5.000 ? 116 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 34.602 22.895 ? 38 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 20.902 15.000 ? 168 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 14.390 15.000 ? 5 'X-RAY DIFFRACTION' ? r_chiral_restr 0.113 0.200 ? 161 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 717 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.290 0.200 ? 378 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.339 0.200 ? 667 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.187 0.200 ? 31 '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 0.228 0.200 ? 46 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.256 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 0.887 1.500 ? 633 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.419 2.000 ? 977 'X-RAY DIFFRACTION' ? r_scbond_it 2.300 3.000 ? 467 'X-RAY DIFFRACTION' ? r_scangle_it 3.375 4.500 ? 406 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.43 _refine_ls_shell.d_res_low 2.50 _refine_ls_shell.number_reflns_R_work 238 _refine_ls_shell.R_factor_R_work 0.3040 _refine_ls_shell.percent_reflns_obs 65.21 _refine_ls_shell.R_factor_R_free 0.5410 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 15 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3D6T _struct.title ;Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase ; _struct.pdbx_descriptor ;Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3D6T _struct_keywords.text ;parkinson's disease, LRRK2, Roc, Roco, GTPase, Kinase, ATP-binding, Disease Mutation, GTP-binding, GTPase activation, Leucine-rich repeat, membrane, nucleotide-binding, parkinson disease, serine/threonine-protein kinase, transferase ; _struct_keywords.pdbx_keywords TRANSFERASE # 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 ? # 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 12 ? LEU A 17 ? GLY B 1346 LEU B 1351 1 ? 6 HELX_P HELX_P2 2 GLY A 63 ? SER A 69 ? GLY B 1397 SER B 1403 1 ? 7 HELX_P HELX_P3 3 HIS A 71 ? ARG A 78 ? HIS B 1405 ARG B 1412 1 ? 8 HELX_P HELX_P4 4 MSE A 97 ? ALA A 108 ? MSE B 1431 ALA B 1442 1 ? 12 # _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 MSE 1 C ? ? ? 1_555 A LYS 2 N ? ? B MSE 1335 B LYS 1336 1_555 ? ? ? ? ? ? ? 1.323 ? covale2 covale ? ? A LEU 3 C ? ? ? 1_555 A MSE 4 N ? ? B LEU 1337 B MSE 1338 1_555 ? ? ? ? ? ? ? 1.325 ? covale3 covale ? ? A MSE 4 C ? ? ? 1_555 A ILE 5 N ? ? B MSE 1338 B ILE 1339 1_555 ? ? ? ? ? ? ? 1.296 ? covale4 covale ? ? A LEU 20 C ? ? ? 1_555 A MSE 21 N ? ? B LEU 1354 B MSE 1355 1_555 ? ? ? ? ? ? ? 1.313 ? covale5 covale ? ? A PHE 74 C ? ? ? 1_555 A MSE 75 N ? ? B PHE 1408 B MSE 1409 1_555 ? ? ? ? ? ? ? 1.340 ? covale6 covale ? ? A MSE 75 C ? ? ? 1_555 A THR 76 N ? ? B MSE 1409 B THR 1410 1_555 ? ? ? ? ? ? ? 1.335 ? covale7 covale ? ? A ALA 96 C ? ? ? 1_555 A MSE 97 N ? ? B ALA 1430 B MSE 1431 1_555 ? ? ? ? ? ? ? 1.329 ? covale8 covale ? ? A MSE 97 C ? ? ? 1_555 A LYS 98 N ? ? B MSE 1431 B LYS 1432 1_555 ? ? ? ? ? ? ? 1.329 ? metalc1 metalc ? ? B MG . MG ? ? ? 1_555 C GDP . O2B ? ? B MG 2 B GDP 1 1_555 ? ? ? ? ? ? ? 2.171 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 3 ? B ? 3 ? # 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 ? parallel A 2 3 ? anti-parallel B 1 2 ? parallel B 2 3 ? 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 MSE A 4 ? ILE A 5 ? MSE B 1338 ILE B 1339 A 2 TRP A 59 ? PHE A 61 ? TRP B 1393 PHE B 1395 A 3 ILE A 37 ? VAL A 39 ? ILE B 1371 VAL B 1373 B 1 TYR A 81 ? ASP A 86 ? TYR B 1415 ASP B 1420 B 2 PRO A 112 ? THR A 118 ? PRO B 1446 THR B 1452 B 3 ALA A 147 ? PHE A 153 ? ALA B 1481 PHE B 1487 # 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 N ILE A 5 ? N ILE B 1339 O TRP A 59 ? O TRP B 1393 A 2 3 O ASP A 60 ? O ASP B 1394 N ASP A 38 ? N ASP B 1372 B 1 2 N TYR A 85 ? N TYR B 1419 O VAL A 116 ? O VAL B 1450 B 2 3 N LEU A 115 ? N LEU B 1449 O HIS A 152 ? O HIS B 1486 # 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 ? ? ? ? 1 'BINDING SITE FOR RESIDUE MG B 2' AC2 Software ? ? ? ? 14 'BINDING SITE FOR RESIDUE GDP B 1' # 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 1 THR A 14 ? THR B 1348 . ? 2_656 ? 2 AC2 14 GLY A 10 ? GLY B 1344 . ? 2_656 ? 3 AC2 14 SER A 11 ? SER B 1345 . ? 2_656 ? 4 AC2 14 GLY A 12 ? GLY B 1346 . ? 2_656 ? 5 AC2 14 LYS A 13 ? LYS B 1347 . ? 2_656 ? 6 AC2 14 THR A 14 ? THR B 1348 . ? 2_656 ? 7 AC2 14 THR A 15 ? THR B 1349 . ? 2_656 ? 8 AC2 14 TYR A 68 ? TYR B 1402 . ? 3_445 ? 9 AC2 14 PRO A 99 ? PRO B 1433 . ? 4_546 ? 10 AC2 14 PHE A 102 ? PHE B 1436 . ? 4_546 ? 11 AC2 14 ASN A 103 ? ASN B 1437 . ? 4_546 ? 12 AC2 14 HIS A 119 ? HIS B 1453 . ? 1_555 ? 13 AC2 14 ASP A 121 ? ASP B 1455 . ? 1_555 ? 14 AC2 14 ASN A 155 ? ASN B 1489 . ? 1_555 ? 15 AC2 14 ALA A 156 ? ALA B 1490 . ? 1_555 ? # _atom_sites.entry_id 3D6T _atom_sites.fract_transf_matrix[1][1] 0.014302 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.006000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.018809 _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] 0.025375 _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 MSE 1 1335 1335 MSE MSE B . n A 1 2 LYS 2 1336 1336 LYS LYS B . n A 1 3 LEU 3 1337 1337 LEU LEU B . n A 1 4 MSE 4 1338 1338 MSE MSE B . n A 1 5 ILE 5 1339 1339 ILE ILE B . n A 1 6 VAL 6 1340 1340 VAL VAL B . n A 1 7 GLY 7 1341 1341 GLY GLY B . n A 1 8 ASN 8 1342 1342 ASN ASN B . n A 1 9 THR 9 1343 1343 THR THR B . n A 1 10 GLY 10 1344 1344 GLY GLY B . n A 1 11 SER 11 1345 1345 SER SER B . n A 1 12 GLY 12 1346 1346 GLY GLY B . n A 1 13 LYS 13 1347 1347 LYS LYS B . n A 1 14 THR 14 1348 1348 THR THR B . n A 1 15 THR 15 1349 1349 THR THR B . n A 1 16 LEU 16 1350 1350 LEU LEU B . n A 1 17 LEU 17 1351 1351 LEU LEU B . n A 1 18 GLN 18 1352 ? ? ? B . n A 1 19 GLN 19 1353 1353 GLN GLN B . n A 1 20 LEU 20 1354 1354 LEU LEU B . n A 1 21 MSE 21 1355 1355 MSE MSE B . n A 1 22 LYS 22 1356 ? ? ? B . n A 1 23 THR 23 1357 ? ? ? B . n A 1 24 LYS 24 1358 ? ? ? B . n A 1 25 LYS 25 1359 ? ? ? B . n A 1 26 SER 26 1360 ? ? ? B . n A 1 27 ASP 27 1361 ? ? ? B . n A 1 28 LEU 28 1362 ? ? ? B . n A 1 29 GLY 29 1363 ? ? ? B . n A 1 30 MSE 30 1364 ? ? ? B . n A 1 31 GLN 31 1365 ? ? ? B . n A 1 32 SER 32 1366 ? ? ? B . n A 1 33 ALA 33 1367 ? ? ? B . n A 1 34 THR 34 1368 ? ? ? B . n A 1 35 VAL 35 1369 ? ? ? B . n A 1 36 GLY 36 1370 1370 GLY GLY B . n A 1 37 ILE 37 1371 1371 ILE ILE B . n A 1 38 ASP 38 1372 1372 ASP ASP B . n A 1 39 VAL 39 1373 1373 VAL VAL B . n A 1 40 LYS 40 1374 1374 LYS LYS B . n A 1 41 ASP 41 1375 1375 ASP ASP B . n A 1 42 TRP 42 1376 1376 TRP TRP B . n A 1 43 PRO 43 1377 1377 PRO PRO B . n A 1 44 ILE 44 1378 ? ? ? B . n A 1 45 GLN 45 1379 ? ? ? B . n A 1 46 ILE 46 1380 ? ? ? B . n A 1 47 ARG 47 1381 ? ? ? B . n A 1 48 ASP 48 1382 ? ? ? B . n A 1 49 LYS 49 1383 ? ? ? B . n A 1 50 ARG 50 1384 ? ? ? B . n A 1 51 LYS 51 1385 ? ? ? B . n A 1 52 ARG 52 1386 ? ? ? B . n A 1 53 ASP 53 1387 ? ? ? B . n A 1 54 LEU 54 1388 1388 LEU LEU B . n A 1 55 VAL 55 1389 1389 VAL VAL B . n A 1 56 LEU 56 1390 1390 LEU LEU B . n A 1 57 ASN 57 1391 ? ? ? B . n A 1 58 VAL 58 1392 1392 VAL VAL B . n A 1 59 TRP 59 1393 1393 TRP TRP B . n A 1 60 ASP 60 1394 1394 ASP ASP B . n A 1 61 PHE 61 1395 1395 PHE PHE B . n A 1 62 ALA 62 1396 1396 ALA ALA B . n A 1 63 GLY 63 1397 1397 GLY GLY B . n A 1 64 ARG 64 1398 1398 ARG ARG B . n A 1 65 GLU 65 1399 1399 GLU GLU B . n A 1 66 GLU 66 1400 1400 GLU GLU B . n A 1 67 PHE 67 1401 1401 PHE PHE B . n A 1 68 TYR 68 1402 1402 TYR TYR B . n A 1 69 SER 69 1403 1403 SER SER B . n A 1 70 THR 70 1404 1404 THR THR B . n A 1 71 HIS 71 1405 1405 HIS HIS B . n A 1 72 PRO 72 1406 1406 PRO PRO B . n A 1 73 HIS 73 1407 1407 HIS HIS B . n A 1 74 PHE 74 1408 1408 PHE PHE B . n A 1 75 MSE 75 1409 1409 MSE MSE B . n A 1 76 THR 76 1410 1410 THR THR B . n A 1 77 GLN 77 1411 1411 GLN GLN B . n A 1 78 ARG 78 1412 1412 ARG ARG B . n A 1 79 ALA 79 1413 1413 ALA ALA B . n A 1 80 LEU 80 1414 1414 LEU LEU B . n A 1 81 TYR 81 1415 1415 TYR TYR B . n A 1 82 LEU 82 1416 1416 LEU LEU B . n A 1 83 ALA 83 1417 1417 ALA ALA B . n A 1 84 VAL 84 1418 1418 VAL VAL B . n A 1 85 TYR 85 1419 1419 TYR TYR B . n A 1 86 ASP 86 1420 1420 ASP ASP B . n A 1 87 LEU 87 1421 1421 LEU LEU B . n A 1 88 SER 88 1422 1422 SER SER B . n A 1 89 LYS 89 1423 1423 LYS LYS B . n A 1 90 GLY 90 1424 1424 GLY GLY B . n A 1 91 GLN 91 1425 1425 GLN GLN B . n A 1 92 ALA 92 1426 1426 ALA ALA B . n A 1 93 GLU 93 1427 1427 GLU GLU B . n A 1 94 VAL 94 1428 1428 VAL VAL B . n A 1 95 ASP 95 1429 1429 ASP ASP B . n A 1 96 ALA 96 1430 1430 ALA ALA B . n A 1 97 MSE 97 1431 1431 MSE MSE B . n A 1 98 LYS 98 1432 1432 LYS LYS B . n A 1 99 PRO 99 1433 1433 PRO PRO B . n A 1 100 TRP 100 1434 1434 TRP TRP B . n A 1 101 LEU 101 1435 1435 LEU LEU B . n A 1 102 PHE 102 1436 1436 PHE PHE B . n A 1 103 ASN 103 1437 1437 ASN ASN B . n A 1 104 ILE 104 1438 1438 ILE ILE B . n A 1 105 LYS 105 1439 1439 LYS LYS B . n A 1 106 ALA 106 1440 1440 ALA ALA B . n A 1 107 ARG 107 1441 1441 ARG ARG B . n A 1 108 ALA 108 1442 1442 ALA ALA B . n A 1 109 SER 109 1443 1443 SER SER B . n A 1 110 SER 110 1444 1444 SER SER B . n A 1 111 SER 111 1445 1445 SER SER B . n A 1 112 PRO 112 1446 1446 PRO PRO B . n A 1 113 VAL 113 1447 1447 VAL VAL B . n A 1 114 ILE 114 1448 1448 ILE ILE B . n A 1 115 LEU 115 1449 1449 LEU LEU B . n A 1 116 VAL 116 1450 1450 VAL VAL B . n A 1 117 GLY 117 1451 1451 GLY GLY B . n A 1 118 THR 118 1452 1452 THR THR B . n A 1 119 HIS 119 1453 1453 HIS HIS B . n A 1 120 LEU 120 1454 1454 LEU LEU B . n A 1 121 ASP 121 1455 1455 ASP ASP B . n A 1 122 VAL 122 1456 1456 VAL VAL B . n A 1 123 SER 123 1457 1457 SER SER B . n A 1 124 ASP 124 1458 1458 ASP ASP B . n A 1 125 GLU 125 1459 ? ? ? B . n A 1 126 LYS 126 1460 ? ? ? B . n A 1 127 GLN 127 1461 ? ? ? B . n A 1 128 ARG 128 1462 ? ? ? B . n A 1 129 LYS 129 1463 ? ? ? B . n A 1 130 ALA 130 1464 ? ? ? B . n A 1 131 CYS 131 1465 ? ? ? B . n A 1 132 MSE 132 1466 ? ? ? B . n A 1 133 SER 133 1467 ? ? ? B . n A 1 134 LYS 134 1468 1468 LYS LYS B . n A 1 135 ILE 135 1469 1469 ILE ILE B . n A 1 136 THR 136 1470 ? ? ? B . n A 1 137 LYS 137 1471 ? ? ? B . n A 1 138 GLU 138 1472 ? ? ? B . n A 1 139 LEU 139 1473 1473 LEU LEU B . n A 1 140 LEU 140 1474 1474 LEU LEU B . n A 1 141 ASN 141 1475 ? ? ? B . n A 1 142 LYS 142 1476 ? ? ? B . n A 1 143 ARG 143 1477 ? ? ? B . n A 1 144 GLY 144 1478 1478 GLY GLY B . n A 1 145 PHE 145 1479 1479 PHE PHE B . n A 1 146 PRO 146 1480 1480 PRO PRO B . n A 1 147 ALA 147 1481 1481 ALA ALA B . n A 1 148 ILE 148 1482 1482 ILE ILE B . n A 1 149 ARG 149 1483 1483 ARG ARG B . n A 1 150 ASP 150 1484 1484 ASP ASP B . n A 1 151 TYR 151 1485 1485 TYR TYR B . n A 1 152 HIS 152 1486 1486 HIS HIS B . n A 1 153 PHE 153 1487 1487 PHE PHE B . n A 1 154 VAL 154 1488 1488 VAL VAL B . n A 1 155 ASN 155 1489 1489 ASN ASN B . n A 1 156 ALA 156 1490 1490 ALA ALA B . n A 1 157 THR 157 1491 1491 THR THR B . n A 1 158 GLU 158 1492 1492 GLU GLU B . n A 1 159 GLU 159 1493 1493 GLU GLU B . n A 1 160 SER 160 1494 1494 SER SER B . n A 1 161 ASP 161 1495 ? ? ? B . n A 1 162 ALA 162 1496 ? ? ? B . n A 1 163 LEU 163 1497 ? ? ? B . n A 1 164 ALA 164 1498 ? ? ? B . n A 1 165 LYS 165 1499 ? ? ? B . n A 1 166 LEU 166 1500 1500 LEU LEU B . n A 1 167 ARG 167 1501 1501 ARG ARG B . n A 1 168 LYS 168 1502 1502 LYS LYS B . n A 1 169 THR 169 1503 1503 THR THR B . n A 1 170 ILE 170 1504 1504 ILE ILE B . n A 1 171 ILE 171 1505 1505 ILE ILE B . 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 2 2 MG MG B . C 3 GDP 1 1 1 GDP GDP B . D 4 HOH 1 1506 1 HOH HOH B . D 4 HOH 2 1507 2 HOH HOH B . D 4 HOH 3 1508 3 HOH HOH B . D 4 HOH 4 1509 4 HOH HOH B . D 4 HOH 5 1510 5 HOH HOH B . D 4 HOH 6 1511 8 HOH HOH B . # 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 1 B MSE 1335 ? MET SELENOMETHIONINE 2 A MSE 4 B MSE 1338 ? MET SELENOMETHIONINE 3 A MSE 21 B MSE 1355 ? MET SELENOMETHIONINE 4 A MSE 75 B MSE 1409 ? MET SELENOMETHIONINE 5 A MSE 97 B MSE 1431 ? MET SELENOMETHIONINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? monomeric 1 2 software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D 2 1,2 A,B,C,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 2 'ABSA (A^2)' 6630 ? 2 MORE -42.7 ? 2 'SSA (A^2)' 13090 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 53.3856420466 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 39.4082957102 # 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 2008-06-10 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2018-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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' Advisory 4 3 'Structure model' 'Refinement description' 5 3 'Structure model' 'Source and taxonomy' 6 4 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' entity_src_gen 2 3 'Structure model' pdbx_unobs_or_zero_occ_atoms 3 3 'Structure model' software 4 4 'Structure model' struct_keywords # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_entity_src_gen.gene_src_strain' 2 3 'Structure model' '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id' 3 3 'Structure model' '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id' 4 3 'Structure model' '_entity_src_gen.pdbx_host_org_strain' 5 3 'Structure model' '_software.classification' 6 3 'Structure model' '_software.contact_author' 7 3 'Structure model' '_software.contact_author_email' 8 3 'Structure model' '_software.date' 9 3 'Structure model' '_software.language' 10 3 'Structure model' '_software.location' 11 3 'Structure model' '_software.name' 12 3 'Structure model' '_software.type' 13 3 'Structure model' '_software.version' 14 4 'Structure model' '_struct_keywords.text' # loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 'X, Y, Z' 2 '-X, Y, -Z' 3 'X+1/2, Y+1/2, Z' 4 '-X+1/2, Y+1/2, -Z' # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.pdbx_refine_id 1 ? refined 31.8868 -8.7054 29.0090 0.1118 0.0893 0.1758 -0.0770 0.0104 -0.1423 38.3732 20.8940 5.8073 -16.6866 -7.1720 -4.6862 0.2686 -1.1778 0.1584 0.5322 0.0198 0.5494 -1.0741 0.0109 -0.2883 'X-RAY DIFFRACTION' 2 ? refined 41.1984 -16.0176 23.8143 0.1221 0.1616 0.1328 0.0528 0.0214 -0.0577 7.6445 11.5705 0.3873 -3.7280 1.4435 0.3536 0.0241 0.0897 -0.0192 0.1579 -0.1615 -0.2721 -0.3169 -0.0116 0.1374 'X-RAY DIFFRACTION' 3 ? refined 30.1860 -16.4987 30.5170 0.1057 0.1335 0.1782 0.0213 0.1652 0.0396 3.7869 5.6450 7.5350 -0.7385 5.2293 0.2940 -0.2819 -0.2808 -0.3533 0.7605 0.1847 0.7599 0.0723 -0.7128 0.0972 'X-RAY DIFFRACTION' 4 ? refined 32.6690 -12.4144 22.9618 0.0631 0.1963 0.1661 -0.0681 0.0445 -0.0653 10.2691 5.4351 15.3384 7.4708 -12.5504 -9.1304 -0.2125 -0.4444 -1.2122 0.1242 -0.4085 0.3411 -0.2207 0.3468 0.6210 'X-RAY DIFFRACTION' 5 ? refined 37.4677 -7.9255 15.4981 0.0486 0.1514 0.1717 0.0168 0.1059 -0.0121 13.6589 29.3068 52.7257 4.5987 -7.1223 34.4869 0.1925 1.5941 0.9887 -1.4705 1.2153 -1.4178 -1.2512 1.3216 -1.4078 'X-RAY DIFFRACTION' 6 ? refined 31.3894 -1.2524 14.7079 0.0416 0.0776 0.2312 -0.0113 0.0176 0.0817 5.6023 18.4098 4.3829 -4.1697 3.7903 2.4548 -0.0631 0.2440 0.6438 0.5860 0.0168 0.1029 0.3653 -0.4653 0.0463 'X-RAY DIFFRACTION' 7 ? refined 24.5734 -1.2527 10.8083 0.0818 0.0846 0.3090 0.0074 0.0071 0.0778 15.5813 5.6768 7.4130 9.2808 3.6538 3.1644 -0.6225 0.2553 0.7466 -0.3679 -0.1582 0.5295 -0.4182 0.6056 0.7807 'X-RAY DIFFRACTION' 8 ? refined 7.6025 -11.2514 12.5676 0.1135 0.1239 0.1518 -0.0279 -0.0154 0.0063 10.5949 4.8580 0.7387 2.4215 0.9096 1.8942 0.3534 0.1070 0.7371 0.0335 -0.2262 0.9263 0.1043 -0.0470 -0.1272 'X-RAY DIFFRACTION' 9 ? refined 2.0613 -6.2718 17.5588 0.0884 0.0420 0.3527 0.0064 0.1341 -0.0693 3.7623 20.0070 9.1305 7.9333 -2.8394 -1.2007 -0.4019 0.7914 -0.4284 -0.4656 0.2923 0.5799 0.3732 -0.3494 0.1096 'X-RAY DIFFRACTION' 10 ? refined 11.9260 -3.1616 13.0041 0.0768 0.0926 0.1558 0.0137 -0.0002 0.0592 1.6847 5.1109 3.4996 0.7692 -0.0131 1.1492 0.0068 0.1465 0.4700 -0.3266 0.1610 0.0995 -0.3348 -0.2177 -0.1678 'X-RAY DIFFRACTION' 11 ? refined -1.0441 -11.3989 9.2270 0.0932 0.0622 0.1655 -0.0057 -0.0008 -0.0089 8.4947 12.1332 4.9460 9.7723 4.0049 6.2581 -0.2981 -0.2316 0.6055 -1.4781 0.1661 1.8460 -0.6227 -0.4752 0.1320 'X-RAY DIFFRACTION' 12 ? refined 8.4244 -2.7430 5.7705 -0.0002 0.0721 0.2085 -0.1017 -0.1351 0.1104 5.4349 13.8121 9.2836 -1.0352 -2.6307 -0.1045 -0.3587 0.8004 0.1447 -1.5163 0.2468 0.3236 -0.5531 -0.5203 0.1119 'X-RAY DIFFRACTION' 13 ? refined 10.9963 -17.4201 2.8060 0.2764 0.0443 -0.0248 0.0114 -0.0350 -0.0365 10.4482 5.1334 3.7085 3.3272 -1.7694 0.3176 -0.3721 0.7620 -0.4408 -1.0271 0.1653 -0.1497 0.3710 -0.2961 0.2068 'X-RAY DIFFRACTION' # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _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.pdbx_refine_id _pdbx_refine_tls_group.selection_details 1 1 B 1335 A 1 B 1339 A 5 ? 'X-RAY DIFFRACTION' ? 2 2 B 1340 A 6 B 1351 A 17 ? 'X-RAY DIFFRACTION' ? 3 3 B 1353 A 19 B 1390 A 56 ? 'X-RAY DIFFRACTION' ? 4 4 B 1392 A 58 B 1396 A 62 ? 'X-RAY DIFFRACTION' ? 5 5 B 1397 A 63 B 1401 A 67 ? 'X-RAY DIFFRACTION' ? 6 6 B 1402 A 68 B 1407 A 73 ? 'X-RAY DIFFRACTION' ? 7 7 B 1408 A 74 B 1414 A 80 ? 'X-RAY DIFFRACTION' ? 8 8 B 1415 A 81 B 1422 A 88 ? 'X-RAY DIFFRACTION' ? 9 9 B 1423 A 89 B 1433 A 99 ? 'X-RAY DIFFRACTION' ? 10 10 B 1434 A 100 B 1453 A 119 ? 'X-RAY DIFFRACTION' ? 11 11 B 1454 A 120 B 1474 A 140 ? 'X-RAY DIFFRACTION' ? 12 12 B 1478 A 144 B 1486 A 152 ? 'X-RAY DIFFRACTION' ? 13 13 B 1487 A 153 B 1505 A 171 ? 'X-RAY DIFFRACTION' ? # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal DENZO . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data reduction' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 2 REFMAC 5.2.0019 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 3 PDB_EXTRACT 3.005 'September 10, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 4 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 B GLN 1352 ? A GLN 18 2 1 Y 1 B LYS 1356 ? A LYS 22 3 1 Y 1 B THR 1357 ? A THR 23 4 1 Y 1 B LYS 1358 ? A LYS 24 5 1 Y 1 B LYS 1359 ? A LYS 25 6 1 Y 1 B SER 1360 ? A SER 26 7 1 Y 1 B ASP 1361 ? A ASP 27 8 1 Y 1 B LEU 1362 ? A LEU 28 9 1 Y 1 B GLY 1363 ? A GLY 29 10 1 Y 1 B MSE 1364 ? A MSE 30 11 1 Y 1 B GLN 1365 ? A GLN 31 12 1 Y 1 B SER 1366 ? A SER 32 13 1 Y 1 B ALA 1367 ? A ALA 33 14 1 Y 1 B THR 1368 ? A THR 34 15 1 Y 1 B VAL 1369 ? A VAL 35 16 1 Y 1 B ILE 1378 ? A ILE 44 17 1 Y 1 B GLN 1379 ? A GLN 45 18 1 Y 1 B ILE 1380 ? A ILE 46 19 1 Y 1 B ARG 1381 ? A ARG 47 20 1 Y 1 B ASP 1382 ? A ASP 48 21 1 Y 1 B LYS 1383 ? A LYS 49 22 1 Y 1 B ARG 1384 ? A ARG 50 23 1 Y 1 B LYS 1385 ? A LYS 51 24 1 Y 1 B ARG 1386 ? A ARG 52 25 1 Y 1 B ASP 1387 ? A ASP 53 26 1 Y 1 B ASN 1391 ? A ASN 57 27 1 Y 1 B GLU 1459 ? A GLU 125 28 1 Y 1 B LYS 1460 ? A LYS 126 29 1 Y 1 B GLN 1461 ? A GLN 127 30 1 Y 1 B ARG 1462 ? A ARG 128 31 1 Y 1 B LYS 1463 ? A LYS 129 32 1 Y 1 B ALA 1464 ? A ALA 130 33 1 Y 1 B CYS 1465 ? A CYS 131 34 1 Y 1 B MSE 1466 ? A MSE 132 35 1 Y 1 B SER 1467 ? A SER 133 36 1 Y 1 B THR 1470 ? A THR 136 37 1 Y 1 B LYS 1471 ? A LYS 137 38 1 Y 1 B GLU 1472 ? A GLU 138 39 1 Y 1 B ASN 1475 ? A ASN 141 40 1 Y 1 B LYS 1476 ? A LYS 142 41 1 Y 1 B ARG 1477 ? A ARG 143 42 1 Y 1 B ASP 1495 ? A ASP 161 43 1 Y 1 B ALA 1496 ? A ALA 162 44 1 Y 1 B LEU 1497 ? A LEU 163 45 1 Y 1 B ALA 1498 ? A ALA 164 46 1 Y 1 B LYS 1499 ? A LYS 165 # 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 # _reflns_scale.group_code 1 #