data_2OMM # _entry.id 2OMM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2OMM pdb_00002omm 10.2210/pdb2omm/pdb RCSB RCSB041323 ? ? WWPDB D_1000041323 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1YJP 'Same peptide, different crystal packing' unspecified PDB 2OLX 'NNQQ, a four residue fragment of GNNQQNY' unspecified PDB 1YJO 'NNQQNY, a six residue fragment of GNNQQNY' unspecified # _pdbx_database_status.entry_id 2OMM _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-01-22 _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.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sawaya, M.R.' 1 'Nelson, R.' 2 'Eisenberg, D.' 3 # _citation.id primary _citation.title 'Atomic structures of amyloid cross-beta spines reveal varied steric zippers.' _citation.journal_abbrev Nature _citation.journal_volume 447 _citation.page_first 453 _citation.page_last 457 _citation.year 2007 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17468747 _citation.pdbx_database_id_DOI 10.1038/nature05695 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sawaya, M.R.' 1 ? primary 'Sambashivan, S.' 2 ? primary 'Nelson, R.' 3 ? primary 'Ivanova, M.I.' 4 ? primary 'Sievers, S.A.' 5 ? primary 'Apostol, M.I.' 6 ? primary 'Thompson, M.J.' 7 ? primary 'Balbirnie, M.' 8 ? primary 'Wiltzius, J.J.' 9 ? primary 'McFarlane, H.T.' 10 ? primary 'Madsen, A.O.' 11 ? primary 'Riekel, C.' 12 ? primary 'Eisenberg, D.' 13 ? # _cell.length_a 23.324 _cell.length_b 4.934 _cell.length_c 37.548 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 2OMM _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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.space_group_name_H-M 'P 21 21 21' _symmetry.entry_id 2OMM _symmetry.Int_Tables_number 19 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _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 syn 'GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35' 836.807 1 ? ? 'residues 7-13' ? 2 water nat water 18.015 3 ? ? ? ? # _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 GNNQQNY _entity_poly.pdbx_seq_one_letter_code_can GNNQQNY _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 ASN n 1 3 ASN n 1 4 GLN n 1 5 GLN n 1 6 ASN n 1 7 TYR n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2OMM _struct_ref.pdbx_db_accession 2OMM _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 2OMM _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 7 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2OMM _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 7 _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 7 # 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 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # _exptl.crystals_number 1 _exptl.entry_id 2OMM _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews ? _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'EVAPORATION, RECRYSTALLIZATION' _exptl_crystal_grow.pH ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;peptide was dissolved at 10 mg/mL in water, quickly filtered, and left to sit at room temperature, EVAPORATION, RECRYSTALLIZATION, temperature 298K ; _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2005-07-16 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.94660 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID13' _diffrn_source.pdbx_wavelength 0.94660 _diffrn_source.pdbx_wavelength_list ? _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID13 # _reflns.entry_id 2OMM _reflns.d_resolution_high 2.000 _reflns.number_obs 380 _reflns.pdbx_Rmerge_I_obs 0.248 _reflns.pdbx_netI_over_sigmaI 4.610 _reflns.percent_possible_obs 96.400 _reflns.B_iso_Wilson_estimate 2.446 _reflns.observed_criterion_sigma_I -3.00 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 19.81 _reflns.number_all ? _reflns.pdbx_Rsym_value ? _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 2.00 2.20 261 ? ? 0.417 2.7 ? ? ? ? 90 98.90 ? 1 2.20 2.50 267 ? ? 0.391 3.3 ? ? ? ? 97 94.20 ? 2 2.50 3.00 193 ? ? 0.301 3.8 ? ? ? ? 69 98.60 ? 3 3.00 ? 307 ? ? 0.13 8.1 ? ? ? ? 101 97.10 ? 4 # _refine.entry_id 2OMM _refine.ls_d_res_high 2.000 _refine.ls_d_res_low 19.810 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 94.660 _refine.ls_number_reflns_obs 372 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_R_factor_obs 0.242 _refine.ls_R_factor_R_work 0.241 _refine.ls_R_factor_R_free 0.252 _refine.ls_percent_reflns_R_free 4.800 _refine.ls_number_reflns_R_free 18 _refine.B_iso_mean 12.533 _refine.aniso_B[1][1] 0.050 _refine.aniso_B[2][2] 0.190 _refine.aniso_B[3][3] -0.240 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.904 _refine.correlation_coeff_Fo_to_Fc_free 0.885 _refine.pdbx_overall_ESU_R 0.382 _refine.pdbx_overall_ESU_R_Free 0.218 _refine.overall_SU_ML 0.141 _refine.overall_SU_B 5.080 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.400 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'pdb entry 1yjp' _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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_overall_phase_error ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 59 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 62 _refine_hist.d_res_high 2.000 _refine_hist.d_res_low 19.810 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 59 0.011 0.021 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 34 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 79 1.544 1.857 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 83 0.635 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6 7.418 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 6 56.115 28.333 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 8 11.183 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 6 0.104 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 74 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 10 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 3 0.123 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 24 0.180 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 23 0.180 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 27 0.085 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 2 0.149 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 9 0.153 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 13 0.159 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 4 0.076 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 45 2.691 2.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 14 0.873 2.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 52 3.309 3.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 34 2.295 2.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 27 2.561 3.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.000 _refine_ls_shell.d_res_low 2.053 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 95.000 _refine_ls_shell.number_reflns_R_work 18 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.22 _refine_ls_shell.R_factor_R_free 0.088 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 1 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs 19 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2OMM _struct.title 'GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2OMM _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' _struct_keywords.text 'steric zipper, glutamine zipper, polar zipper, asparagine zipper, PROTEIN FIBRIL' # 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 _struct_biol.details ;One sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the b axis. The second sheet of the steric zipper can be generated by application of the crystallographic operator -X+1,-1/2+Y,1/2-Z, and repeated unit cell translations of this strand along the b axis. ; _struct_biol.pdbx_parent_biol_id ? # _atom_sites.entry_id 2OMM _atom_sites.fract_transf_matrix[1][1] 0.042874 _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] 0.202675 _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] 0.026633 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . GLY A 1 1 ? 2.913 1.693 2.714 1.00 23.50 ? 1 GLY A N 1 ATOM 2 C CA . GLY A 1 1 ? 3.184 2.028 4.142 1.00 18.20 ? 1 GLY A CA 1 ATOM 3 C C . GLY A 1 1 ? 4.165 3.179 4.279 1.00 15.44 ? 1 GLY A C 1 ATOM 4 O O . GLY A 1 1 ? 4.468 3.883 3.307 1.00 10.77 ? 1 GLY A O 1 ATOM 5 N N . ASN A 1 2 ? 4.661 3.366 5.498 1.00 11.68 ? 2 ASN A N 1 ATOM 6 C CA . ASN A 1 2 ? 5.625 4.413 5.776 1.00 13.34 ? 2 ASN A CA 1 ATOM 7 C C . ASN A 1 2 ? 6.968 3.831 5.425 1.00 12.48 ? 2 ASN A C 1 ATOM 8 O O . ASN A 1 2 ? 7.194 2.612 5.642 1.00 13.23 ? 2 ASN A O 1 ATOM 9 C CB . ASN A 1 2 ? 5.582 4.865 7.247 1.00 14.57 ? 2 ASN A CB 1 ATOM 10 C CG . ASN A 1 2 ? 4.169 5.210 7.727 1.00 16.09 ? 2 ASN A CG 1 ATOM 11 O OD1 . ASN A 1 2 ? 3.803 6.385 7.853 1.00 10.16 ? 2 ASN A OD1 1 ATOM 12 N ND2 . ASN A 1 2 ? 3.371 4.173 8.003 1.00 14.56 ? 2 ASN A ND2 1 ATOM 13 N N . ASN A 1 3 ? 7.851 4.703 4.941 1.00 6.86 ? 3 ASN A N 1 ATOM 14 C CA . ASN A 1 3 ? 9.134 4.342 4.336 1.00 10.42 ? 3 ASN A CA 1 ATOM 15 C C . ASN A 1 3 ? 10.304 4.867 5.145 1.00 12.24 ? 3 ASN A C 1 ATOM 16 O O . ASN A 1 3 ? 10.370 6.078 5.367 1.00 7.66 ? 3 ASN A O 1 ATOM 17 C CB . ASN A 1 3 ? 9.189 4.966 2.915 1.00 11.62 ? 3 ASN A CB 1 ATOM 18 C CG . ASN A 1 3 ? 10.480 4.637 2.140 1.00 8.88 ? 3 ASN A CG 1 ATOM 19 O OD1 . ASN A 1 3 ? 10.875 3.475 2.004 1.00 11.30 ? 3 ASN A OD1 1 ATOM 20 N ND2 . ASN A 1 3 ? 11.134 5.672 1.615 1.00 12.04 ? 3 ASN A ND2 1 ATOM 21 N N . GLN A 1 4 ? 11.177 3.963 5.627 1.00 7.39 ? 4 GLN A N 1 ATOM 22 C CA . GLN A 1 4 ? 12.501 4.342 6.143 1.00 8.98 ? 4 GLN A CA 1 ATOM 23 C C . GLN A 1 4 ? 13.585 3.685 5.261 1.00 11.18 ? 4 GLN A C 1 ATOM 24 O O . GLN A 1 4 ? 13.535 2.483 4.970 1.00 11.96 ? 4 GLN A O 1 ATOM 25 C CB . GLN A 1 4 ? 12.710 3.961 7.602 1.00 9.59 ? 4 GLN A CB 1 ATOM 26 C CG . GLN A 1 4 ? 13.939 4.620 8.226 1.00 7.26 ? 4 GLN A CG 1 ATOM 27 C CD . GLN A 1 4 ? 14.118 4.300 9.709 1.00 10.24 ? 4 GLN A CD 1 ATOM 28 O OE1 . GLN A 1 4 ? 14.287 3.138 10.106 1.00 7.21 ? 4 GLN A OE1 1 ATOM 29 N NE2 . GLN A 1 4 ? 14.095 5.337 10.533 1.00 7.93 ? 4 GLN A NE2 1 ATOM 30 N N . GLN A 1 5 ? 14.515 4.501 4.774 1.00 12.07 ? 5 GLN A N 1 ATOM 31 C CA . GLN A 1 5 ? 15.597 4.025 3.935 1.00 12.33 ? 5 GLN A CA 1 ATOM 32 C C . GLN A 1 5 ? 16.894 4.578 4.519 1.00 13.41 ? 5 GLN A C 1 ATOM 33 O O . GLN A 1 5 ? 17.117 5.804 4.556 1.00 12.86 ? 5 GLN A O 1 ATOM 34 C CB . GLN A 1 5 ? 15.385 4.436 2.477 1.00 13.09 ? 5 GLN A CB 1 ATOM 35 C CG . GLN A 1 5 ? 14.226 3.656 1.808 1.00 15.38 ? 5 GLN A CG 1 ATOM 36 C CD . GLN A 1 5 ? 14.017 4.001 0.349 1.00 13.93 ? 5 GLN A CD 1 ATOM 37 O OE1 . GLN A 1 5 ? 14.241 5.132 -0.084 1.00 20.44 ? 5 GLN A OE1 1 ATOM 38 N NE2 . GLN A 1 5 ? 13.568 3.037 -0.409 1.00 12.52 ? 5 GLN A NE2 1 ATOM 39 N N . ASN A 1 6 ? 17.738 3.659 4.983 1.00 12.89 ? 6 ASN A N 1 ATOM 40 C CA . ASN A 1 6 ? 19.001 4.007 5.610 1.00 15.89 ? 6 ASN A CA 1 ATOM 41 C C . ASN A 1 6 ? 20.166 3.465 4.778 1.00 17.30 ? 6 ASN A C 1 ATOM 42 O O . ASN A 1 6 ? 20.683 2.385 5.043 1.00 15.29 ? 6 ASN A O 1 ATOM 43 C CB . ASN A 1 6 ? 19.045 3.471 7.045 1.00 15.51 ? 6 ASN A CB 1 ATOM 44 C CG . ASN A 1 6 ? 17.806 3.831 7.845 1.00 16.34 ? 6 ASN A CG 1 ATOM 45 O OD1 . ASN A 1 6 ? 17.647 4.964 8.293 1.00 12.19 ? 6 ASN A OD1 1 ATOM 46 N ND2 . ASN A 1 6 ? 16.929 2.846 8.054 1.00 16.35 ? 6 ASN A ND2 1 ATOM 47 N N . TYR A 1 7 ? 20.556 4.232 3.766 1.00 20.56 ? 7 TYR A N 1 ATOM 48 C CA . TYR A 1 7 ? 21.652 3.845 2.865 1.00 21.50 ? 7 TYR A CA 1 ATOM 49 C C . TYR A 1 7 ? 22.964 4.223 3.522 1.00 22.07 ? 7 TYR A C 1 ATOM 50 O O . TYR A 1 7 ? 22.989 5.144 4.356 1.00 18.72 ? 7 TYR A O 1 ATOM 51 C CB . TYR A 1 7 ? 21.608 4.590 1.535 1.00 22.54 ? 7 TYR A CB 1 ATOM 52 C CG . TYR A 1 7 ? 20.253 4.870 0.918 1.00 23.05 ? 7 TYR A CG 1 ATOM 53 C CD1 . TYR A 1 7 ? 19.510 6.005 1.285 1.00 23.43 ? 7 TYR A CD1 1 ATOM 54 C CD2 . TYR A 1 7 ? 19.751 4.065 -0.095 1.00 21.96 ? 7 TYR A CD2 1 ATOM 55 C CE1 . TYR A 1 7 ? 18.285 6.292 0.691 1.00 23.07 ? 7 TYR A CE1 1 ATOM 56 C CE2 . TYR A 1 7 ? 18.516 4.338 -0.693 1.00 23.14 ? 7 TYR A CE2 1 ATOM 57 C CZ . TYR A 1 7 ? 17.791 5.460 -0.296 1.00 23.59 ? 7 TYR A CZ 1 ATOM 58 O OH . TYR A 1 7 ? 16.579 5.744 -0.886 1.00 21.70 ? 7 TYR A OH 1 ATOM 59 O OXT . TYR A 1 7 ? 24.019 3.659 3.211 1.00 24.06 ? 7 TYR A OXT 1 HETATM 60 O O . HOH B 2 . ? 22.632 5.806 8.997 1.00 22.63 ? 8 HOH A O 1 HETATM 61 O O . HOH B 2 . ? 22.674 3.931 7.114 1.00 21.88 ? 9 HOH A O 1 HETATM 62 O O . HOH B 2 . ? 25.212 4.567 5.603 1.00 30.06 ? 10 HOH A O 1 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 1 1 GLY GLY A . n A 1 2 ASN 2 2 2 ASN ASN A . n A 1 3 ASN 3 3 3 ASN ASN A . n A 1 4 GLN 4 4 4 GLN GLN A . n A 1 5 GLN 5 5 5 GLN GLN A . n A 1 6 ASN 6 6 6 ASN ASN A . n A 1 7 TYR 7 7 7 TYR TYR 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 8 1 HOH HOH A . B 2 HOH 2 9 2 HOH HOH A . B 2 HOH 3 10 3 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 _pdbx_struct_assembly_gen.asym_id_list A,B # 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' 1_565 x,y+1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4.9340000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_645 -x+1,y-1/2,-z+1/2 -1.0000000000 0.0000000000 0.0000000000 23.3240000000 0.0000000000 1.0000000000 0.0000000000 -2.4670000000 0.0000000000 0.0000000000 -1.0000000000 18.7740000000 4 'crystal symmetry operation' 3_655 -x+1,y+1/2,-z+1/2 -1.0000000000 0.0000000000 0.0000000000 23.3240000000 0.0000000000 1.0000000000 0.0000000000 2.4670000000 0.0000000000 0.0000000000 -1.0000000000 18.7740000000 # 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 2007-01-30 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2023-08-30 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 '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' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_initial_refinement_model # 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' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' # 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 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html ? ? 1 PHASER . ? other 'R. J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 2 REFMAC . ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 3 PDB_EXTRACT 2.000 'April. 3, 2006' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 4 XDS . ? ? ? ? 'data reduction' ? ? ? 5 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ASN N N N N 1 ASN CA C N S 2 ASN C C N N 3 ASN O O N N 4 ASN CB C N N 5 ASN CG C N N 6 ASN OD1 O N N 7 ASN ND2 N N N 8 ASN OXT O N N 9 ASN H H N N 10 ASN H2 H N N 11 ASN HA H N N 12 ASN HB2 H N N 13 ASN HB3 H N N 14 ASN HD21 H N N 15 ASN HD22 H N N 16 ASN HXT H N N 17 GLN N N N N 18 GLN CA C N S 19 GLN C C N N 20 GLN O O N N 21 GLN CB C N N 22 GLN CG C N N 23 GLN CD C N N 24 GLN OE1 O N N 25 GLN NE2 N N N 26 GLN OXT O N N 27 GLN H H N N 28 GLN H2 H N N 29 GLN HA H N N 30 GLN HB2 H N N 31 GLN HB3 H N N 32 GLN HG2 H N N 33 GLN HG3 H N N 34 GLN HE21 H N N 35 GLN HE22 H N N 36 GLN HXT H N N 37 GLY N N N N 38 GLY CA C N N 39 GLY C C N N 40 GLY O O N N 41 GLY OXT O N N 42 GLY H H N N 43 GLY H2 H N N 44 GLY HA2 H N N 45 GLY HA3 H N N 46 GLY HXT H N N 47 HOH O O N N 48 HOH H1 H N N 49 HOH H2 H N N 50 TYR N N N N 51 TYR CA C N S 52 TYR C C N N 53 TYR O O N N 54 TYR CB C N N 55 TYR CG C Y N 56 TYR CD1 C Y N 57 TYR CD2 C Y N 58 TYR CE1 C Y N 59 TYR CE2 C Y N 60 TYR CZ C Y N 61 TYR OH O N N 62 TYR OXT O N N 63 TYR H H N N 64 TYR H2 H N N 65 TYR HA H N N 66 TYR HB2 H N N 67 TYR HB3 H N N 68 TYR HD1 H N N 69 TYR HD2 H N N 70 TYR HE1 H N N 71 TYR HE2 H N N 72 TYR HH H N N 73 TYR HXT H N N 74 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ASN N CA sing N N 1 ASN N H sing N N 2 ASN N H2 sing N N 3 ASN CA C sing N N 4 ASN CA CB sing N N 5 ASN CA HA sing N N 6 ASN C O doub N N 7 ASN C OXT sing N N 8 ASN CB CG sing N N 9 ASN CB HB2 sing N N 10 ASN CB HB3 sing N N 11 ASN CG OD1 doub N N 12 ASN CG ND2 sing N N 13 ASN ND2 HD21 sing N N 14 ASN ND2 HD22 sing N N 15 ASN OXT HXT sing N N 16 GLN N CA sing N N 17 GLN N H sing N N 18 GLN N H2 sing N N 19 GLN CA C sing N N 20 GLN CA CB sing N N 21 GLN CA HA sing N N 22 GLN C O doub N N 23 GLN C OXT sing N N 24 GLN CB CG sing N N 25 GLN CB HB2 sing N N 26 GLN CB HB3 sing N N 27 GLN CG CD sing N N 28 GLN CG HG2 sing N N 29 GLN CG HG3 sing N N 30 GLN CD OE1 doub N N 31 GLN CD NE2 sing N N 32 GLN NE2 HE21 sing N N 33 GLN NE2 HE22 sing N N 34 GLN OXT HXT sing N N 35 GLY N CA sing N N 36 GLY N H sing N N 37 GLY N H2 sing N N 38 GLY CA C sing N N 39 GLY CA HA2 sing N N 40 GLY CA HA3 sing N N 41 GLY C O doub N N 42 GLY C OXT sing N N 43 GLY OXT HXT sing N N 44 HOH O H1 sing N N 45 HOH O H2 sing N N 46 TYR N CA sing N N 47 TYR N H sing N N 48 TYR N H2 sing N N 49 TYR CA C sing N N 50 TYR CA CB sing N N 51 TYR CA HA sing N N 52 TYR C O doub N N 53 TYR C OXT sing N N 54 TYR CB CG sing N N 55 TYR CB HB2 sing N N 56 TYR CB HB3 sing N N 57 TYR CG CD1 doub Y N 58 TYR CG CD2 sing Y N 59 TYR CD1 CE1 sing Y N 60 TYR CD1 HD1 sing N N 61 TYR CD2 CE2 doub Y N 62 TYR CD2 HD2 sing N N 63 TYR CE1 CZ doub Y N 64 TYR CE1 HE1 sing N N 65 TYR CE2 CZ sing Y N 66 TYR CE2 HE2 sing N N 67 TYR CZ OH sing N N 68 TYR OH HH sing N N 69 TYR OXT HXT sing N N 70 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1YJP _pdbx_initial_refinement_model.details 'pdb entry 1yjp' #