data_wwPDB_remediated_restraints_file_for_PDB_entry_2hmd # This wwPDB archive file contains, for PDB entry 2hmd: # # - 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, WF Vranken, C Schulte, J Lin, JR Wedell, CJ Penkett, GW Vuister, # G Vriend, JL Markley, and EL Ulrich (2009). The NMR Restraints Grid at BMRB for # 5,266 Protein and Nucleic Acid PDB Entries. J Biomol. NMR 45, 389–396. save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID rr_2hmd _Entry.Title "wwPDB remediated NMR restraints for PDB entry 2hmd" _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 2hmd" save_ save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_2hmd _Assembly.ID 1 _Assembly.Name 2hmd _Assembly.Number_of_components 2 _Assembly.Organic_ligands 0 _Assembly.Metal_ions 0 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state "not present" _Assembly.Molecular_mass 7528.80064 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 dodecamer with interstrand cross link" 1 $DNA_dodecamer_with_interstrand_cross_link A . no . . . . . . rr_2hmd 1 2 "DNA dodecamer with interstrand cross link 2" 2 $DNA_dodecamer_with_interstrand_cross_link_2 B . no . . . . . . rr_2hmd 1 stop_ save_ save_DNA_dodecamer_with_interstrand_cross_link _Entity.Sf_category entity _Entity.Sf_framecode DNA_dodecamer_with_interstrand_cross_link _Entity.Entry_ID rr_2hmd _Entity.ID 1 _Entity.Name DNA_dodecamer_with_interstrand_cross_link _Entity.Type non-polymer _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_chirality yes _Entity.Nstd_linkage yes _Entity.Nonpolymer_comp_ID DG _Entity.Nonpolymer_comp_label $chem_comp_DG _Entity.Number_of_monomers 12 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 1 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 . DG . rr_2hmd 1 2 . DC . rr_2hmd 1 3 . DT . rr_2hmd 1 4 . DA . rr_2hmd 1 5 . DG . rr_2hmd 1 6 . DC . rr_2hmd 1 7 . 2EG . rr_2hmd 1 8 . DA . rr_2hmd 1 9 . DG . rr_2hmd 1 10 . DT . rr_2hmd 1 11 . DC . rr_2hmd 1 12 . DC . rr_2hmd 1 stop_ save_ save_DNA_dodecamer_with_interstrand_cross_link_2 _Entity.Sf_category entity _Entity.Sf_framecode DNA_dodecamer_with_interstrand_cross_link_2 _Entity.Entry_ID rr_2hmd _Entity.ID 2 _Entity.Name DNA_dodecamer_with_interstrand_cross_link_2 _Entity.Type non-polymer _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_chirality yes _Entity.Nstd_linkage yes _Entity.Nonpolymer_comp_ID DG _Entity.Nonpolymer_comp_label $chem_comp_DG _Entity.Number_of_monomers 12 _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 . DG . rr_2hmd 2 2 . DG . rr_2hmd 2 3 . DA . rr_2hmd 2 4 . DC . rr_2hmd 2 5 . DT . rr_2hmd 2 6 . DC . rr_2hmd 2 7 . 2EG . rr_2hmd 2 8 . DC . rr_2hmd 2 9 . DT . rr_2hmd 2 10 . DA . rr_2hmd 2 11 . DG . rr_2hmd 2 12 . DC . rr_2hmd 2 stop_ save_ save_chem_comp_2EG _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_2EG _Chem_comp.Entry_ID rr_2hmd _Chem_comp.ID 2EG _Chem_comp.Name "2'-DEOXY-N-ETHYLGUANOSINE 5'-PHOSPHATE" _Chem_comp.Type non-polymer _Chem_comp.PDB_code 2EG _Chem_comp.Formal_charge 0 _Chem_comp.Paramagnetic no _Chem_comp.Aromatic yes _Chem_comp.Formula "C12 H18 N5 O7 P" _Chem_comp.Formula_weight 375.27726 save_ save_conformer_statistics _Conformer_stat_list.Sf_category conformer_statistics _Conformer_stat_list.Sf_framecode conformer_statistics _Conformer_stat_list.Entry_ID rr_2hmd _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 1 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_2hmd _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 2hmd.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 rr_2hmd 1 1 2hmd.mr . . AMBER 2 distance NOE simple 0 rr_2hmd 1 1 2hmd.mr . . "MR format" 3 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_2hmd 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_2hmd _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 DNA 11-JUL-06 2HMD *TITLE STEREOCHEMISTRY MODULATES STABILITY OF REDUCED INTER-STRAND *TITLE 2 CROSS-LINKS ARISING FROM R- AND S-ALPHA-METHYL-GAMMA-OH-1, *TITLE 3 N2-PROPANO-2'-DEOXYGUANINE IN THE 5'-CPG-3' DNA SEQUENCE *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: DNA DODECAMER WITH INTERSTRAND CROSS-LINK; *COMPND 3 CHAIN: A; *COMPND 4 ENGINEERED: YES; *COMPND 5 OTHER_DETAILS: G7 OF CHAIN A AND B LINKED; *COMPND 6 MOL_ID: 2; *COMPND 7 MOLECULE: DNA DODECAMER WITH INTERSTRAND CROSS-LINK; *COMPND 8 CHAIN: B; *COMPND 9 ENGINEERED: YES; *COMPND 10 OTHER_DETAILS: G7 OF CHAIN A AND B LINKED *SOURCE MOL_ID: 1; *SOURCE 2 SYNTHETIC: YES; *SOURCE 3 MOL_ID: 2; *SOURCE 4 SYNTHETIC: YES *KEYWDS CROTONALDEHYDE INTERSTRAND DNA CROSS-LINK *EXPDTA NMR, MINIMIZED AVERAGE STRUCTURE *AUTHOR Y.-J.CHO, I.D.KOZEKOV, T.M.HARRIS, C.J.RIZZO, M.P.STONE *REVDAT 1 13-MAR-07 2HMD 0 ; save_