data_wwPDB_remediated_restraints_file_for_PDB_entry_108d # This wwPDB archive file contains, for PDB entry 108d: # # - Sequence information from the PDB mmCIF file # - NMR restraints from the PDB MR file # # In this file, the NMR restraints share the same atom names as in the coordinate # file, and in this way can differ from the data deposited at the wwPDB. To achieve # this aim, the NMR restraints were parsed from their original format files, and # the coordinates and NMR restraints information were subsequently harmonized. # # Due to the complexity of this harmonization process, minor modifications could # have occurred to the NMR restraints information, or data could have been lost # because of parsing or conversion errors. The PDB file remains the # authoritative reference for the atomic coordinates and the originally deposited # restraints files remain the primary reference for these data. # # This file is generated as part of the wwPDB at the BioMagResBank (BMRB) in # collaboration with the PDBe (formerly MSD) group at the European # Bioinformatics Institute (EBI) and the CMBI/IMM group at the Radboud # University of Nijmegen. # # Several software packages were used to produce this file: # # - Wattos (BMRB and CMBI/IMM). # - FormatConverter and NMRStarExport (PDBe). # - CCPN framework (http://www.ccpn.ac.uk/). # # More information about this process can be found in the references below. # Please cite the original reference for this PDB entry. # # JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL # Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED # containing converted and filtered sets of experimental NMR restraints and # coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12. # # WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL # Markley, J Ionides, ED Laue (2005). The CCPN data model for NMR spectroscopy: # development of a software pipeline. Proteins 59, 687-696. # # JF Doreleijers, W Vranken, C Penkett, J Lin, CF Schulte, G Vuister, G Vriend, # JL Markley, EL Ulrich. BioMagResBank database `NMR Restraints Grid` with # curated sets of experimental NMR restraints for over 4,000 protein and nucleic # acid PDB entries. (in preparation) save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID rr_108d _Entry.Title "wwPDB remediated NMR restraints for PDB entry 108d" _Entry.NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.Details "Contains the remediated restraint lists and coordinates for PDB entry 108d" save_ save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_108d _Assembly.ID 1 _Assembly.Name 108d _Assembly.Number_of_components 3 _Assembly.Organic_ligands 1 _Assembly.Metal_ions 0 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state "not present" _Assembly.Molecular_mass 5766.27336 loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _Entity_assembly.Asym_ID _Entity_assembly.PDB_chain_ID _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Magnetic_equivalence_group_code _Entity_assembly.Role _Entity_assembly.Details _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 "DNA 5 D CP GP CP TP AP GP CP G 3" 1 $DNA__5__D__CP_GP_CP_TP_AP_GP_CP_G__3__ A . no . . . . . . rr_108d 1 2 "DNA 5 D CP GP CP TP AP GP CP G 3" 1 $DNA__5__D__CP_GP_CP_TP_AP_GP_CP_G__3__ B . no . . . . . . rr_108d 1 3 "1 1 4 4 8 8 TETRAMETHYL 4 8 DIAZAUNDECAMETHYLENE BIS 4 3 METHYL 2 3 DIHYDR" 2 $1_1__4_4_8_8_TETRAMETHYL_4_8_DIAZAUNDECAMETHYLENE__BIS_4_3_METHYL_2_3_DIHYDR C . no . . . . . . rr_108d 1 stop_ save_ save_DNA__5__D__CP_GP_CP_TP_AP_GP_CP_G__3__ _Entity.Sf_category entity _Entity.Sf_framecode DNA__5__D__CP_GP_CP_TP_AP_GP_CP_G__3__ _Entity.Entry_ID rr_108d _Entity.ID 1 _Entity.Name DNA__5__D__CP_GP_CP_TP_AP_GP_CP_G__3__ _Entity.Type polymer _Entity.Polymer_type polydeoxyribonucleotide _Entity.Polymer_strand_ID A,B _Entity.Polymer_seq_one_letter_code CGCTAGCG _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer no _Entity.Nstd_chirality yes _Entity.Nstd_linkage no _Entity.Number_of_monomers 8 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 1 _Entity.Formula_weight 2485.55798 loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . DC . rr_108d 1 2 . DG . rr_108d 1 3 . DC . rr_108d 1 4 . DT . rr_108d 1 5 . DA . rr_108d 1 6 . DG . rr_108d 1 7 . DC . rr_108d 1 8 . DG . rr_108d 1 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . DC 1 1 rr_108d 1 . DG 2 2 rr_108d 1 . DC 3 3 rr_108d 1 . DT 4 4 rr_108d 1 . DA 5 5 rr_108d 1 . DG 6 6 rr_108d 1 . DC 7 7 rr_108d 1 . DG 8 8 rr_108d 1 stop_ save_ save_1_1__4_4_8_8_TETRAMETHYL_4_8_DIAZAUNDECAMETHYLENE__BIS_4_3_METHYL_2_3_DIHYDR _Entity.Sf_category entity _Entity.Sf_framecode 1_1__4_4_8_8_TETRAMETHYL_4_8_DIAZAUNDECAMETHYLENE__BIS_4_3_METHYL_2_3_DIHYDR _Entity.Entry_ID rr_108d _Entity.ID 2 _Entity.Name 1_1__4_4_8_8_TETRAMETHYL_4_8_DIAZAUNDECAMETHYLENE__BIS_4_3_METHYL_2_3_DIHYDR _Entity.Type non-polymer _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_chirality yes _Entity.Nstd_linkage no _Entity.Nonpolymer_comp_ID TOT _Entity.Nonpolymer_comp_label $chem_comp_TOT _Entity.Number_of_monomers 1 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 2 loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . TOT . rr_108d 2 stop_ save_ save_chem_comp_TOT _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_TOT _Chem_comp.Entry_ID rr_108d _Chem_comp.ID TOT _Chem_comp.Name 1,1-(4,4,8,8-TETRAMETHYL-4,8-DIAZAUNDECAMETHYLENE)-BIS-4-3-METHYL-2,3-DIHYDRO-(BENZO-1,3-THIAZOLE)-2-METHYLIDENE)-QUINOLINIUM _Chem_comp.Type non-polymer _Chem_comp.PDB_code TOT _Chem_comp.Formal_charge 4 _Chem_comp.Paramagnetic no _Chem_comp.Aromatic yes _Chem_comp.Formula "C49 H58 N6 S2" _Chem_comp.Formula_weight 795.1574 save_ save_conformer_statistics _Conformer_stat_list.Sf_category conformer_statistics _Conformer_stat_list.Sf_framecode conformer_statistics _Conformer_stat_list.Entry_ID rr_108d _Conformer_stat_list.ID 1 _Conformer_stat_list.Conf_family_coord_set_ID 1 _Conformer_stat_list.Conf_family_coord_set_label $Original_constraints_and_structures _Conformer_stat_list.Conformer_submitted_total_num 40 save_ save_global_Org_file_characteristics _Constraint_stat_list.Sf_framecode global_Org_file_characteristics _Constraint_stat_list.Sf_category constraint_statistics _Constraint_stat_list.Entry_ID rr_108d _Constraint_stat_list.ID 1 loop_ _Constraint_file.ID _Constraint_file.Constraint_filename _Constraint_file.Software_ID _Constraint_file.Software_label _Constraint_file.Software_name _Constraint_file.Block_ID _Constraint_file.Constraint_type _Constraint_file.Constraint_subtype _Constraint_file.Constraint_subsubtype _Constraint_file.Constraint_number _Constraint_file.Entry_ID _Constraint_file.Constraint_stat_list_ID 1 108d.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 rr_108d 1 1 108d.mr . . "MR format" 2 distance "hydrogen bond" simple 0 rr_108d 1 1 108d.mr . . "MR format" 3 comment "Not applicable" "Not applicable" 0 rr_108d 1 1 108d.mr . . "MR format" 4 distance NOE simple 0 rr_108d 1 1 108d.mr . . "MR format" 5 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_108d 1 stop_ save_ save_MR_file_comment_1 _Org_constr_file_comment.Sf_framecode MR_file_comment_1 _Org_constr_file_comment.Sf_category org_constr_file_comment _Org_constr_file_comment.Entry_ID rr_108d _Org_constr_file_comment.ID 1 _Org_constr_file_comment.Constraint_file_ID 1 _Org_constr_file_comment.Block_ID 1 _Org_constr_file_comment.Details "Generated by Wattos" _Org_constr_file_comment.Comment ; *HEADER DEOXYRIBONUCLEIC ACID 31-JAN-95 108D *COMPND DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G-3') COMPLEXED WITH THE *COMPND 2 BISINTERCALATING DYE 1,1-(4,4,8,8-TETRAMETHYL-4,8- *COMPND 3 DIAZAUNDECAMETHYLENE)-BIS-4-(3-METHYL-2,3-DIHYDRO-(BENZO- *COMPND 4 1,3-THIAZOLE)-2-METHYLIDENE)-QUINOLINIUM TETRAIODIDE (TOTO) *COMPND 5 (NMR, 40 STRUCTURES) *SOURCE SYNTHETIC *EXPDTA NMR, 40 STRUCTURES *AUTHOR H.P.SPIELMANN,D.E.WEMMER,J.P.JACOBSEN *REVDAT 1 03-JUN-95 108D 0 REMARK REMARK start NOE derived interpronon distance restraints. REMARK BOUNDS DISTANCES ARE IN ANGSTROMS REMARK FORMAT FOR ATOM NAME IS SEVEN CHAR REMARK CONSISTING OF FOUR CHAR (a4) FOR THE SPECIFIC ATOM REMARK FOLLOWED BY THREE CHAR (i3) FOR THE SPECIFIC RESIDUE REMARK RESIDUES MAP TO THE PDB FILE AS FOLLOWS: REMARK REMARK CONSTRAINT PDB REMARK FILE FILE REMARK RESIDUE RESIDUE REMARK NUMBER NUMBER REMARK 1 == 1 REMARK 2 == 2 REMARK 3 == 3 REMARK 4 == 4 REMARK 5 == 5 REMARK 6 == 6 REMARK 7 == 7 REMARK 8 == 8 REMARK 9 == 1B REMARK 10 == 2B REMARK 11 == 3B REMARK 12 == 4B REMARK 13 == 5B REMARK 14 == 6B REMARK 15 == 7B REMARK 16 == 8B REMARK 17 == 1C REMARK 18 == 2C REMARK 19 == 3C REMARK 20 == 4C REMARK 21 == 5C REMARK 22 == 6C REMARK 23 == 7C REMARK REMARK restraints generated by direct inspection of spectra REMARK REMARK LOWER UPPER REMARK ATOM 1 ATOM 2 BOUND BOUND ; save_ save_MR_file_comment_3 _Org_constr_file_comment.Sf_framecode MR_file_comment_3 _Org_constr_file_comment.Sf_category org_constr_file_comment _Org_constr_file_comment.Entry_ID rr_108d _Org_constr_file_comment.ID 2 _Org_constr_file_comment.Constraint_file_ID 1 _Org_constr_file_comment.Block_ID 3 _Org_constr_file_comment.Details "Generated by Wattos" _Org_constr_file_comment.Comment ; REMARK REMARK H2* 4 is a pseudo atom at the geometric center of REMARK the thymidine residue 4 1H2' and 2H2' protons. REMARK REMARK H2* 12 is a pseudo atom at the geometric center of REMARK the thymidine residue 12 1H2' and 2H2' protons. REMARK REMARK restraints generated by using the randmardi REMARK procedure of the program MARDIGRAS. NOESY data for both upper REMARK and lower sides of the diagonal for five mixing times (25 ms, 50 REMARK ms, 100 ms, 150 ms, 200 ms) corrected for T1 relaxation was REMARK used. Randmardi was implemented using 30 cycles for each of the REMARK ten data sets where the random noise level was set to between REMARK one and five times the integrated intensity of the smallest REMARK cross peak in the spectrum. The results were combined using the REMARK program AVGBNDS (Liu, H., James, T.L. University of California, REMARK San Francisco), and the lower and upper bounds expressed as the REMARK average calculated interproton distance +/- one standard REMARK deviation for that proton pair. The upper bounds were furthur REMARK modified by adding an extra 0.2 Angsroms to them. The bounds for REMARK symmetry related restraints were averaged. The correlation time REMARK used in the relaxation matrix calculations was 3.75ns. REMARK REMARK REMARK LOWER UPPER REMARK ATOM 1 ATOM 2 BOUND BOUND ; save_