data_wwPDB_remediated_restraints_file_for_PDB_entry_214d

# This wwPDB archive file contains, for PDB entry 214d:
#
# - 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_214d
   _Entry.Title                        "wwPDB remediated NMR restraints for PDB entry 214d"
   _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 214d"

save_


save_assembly
   _Assembly.Sf_category            assembly
   _Assembly.Sf_framecode           assembly
   _Assembly.Entry_ID               rr_214d
   _Assembly.ID                     1
   _Assembly.Name                   214d
   _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         6866.33202

   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 AP TP AP TP AP GP CP C 3"    1 $DNA__5__D__CP_GP_CP_AP_TP_AP_TP_AP_GP_CP_C__3__     A . no . . . . . . rr_214d 1 
      2 "DNA 5 D GP GP CP TP AP T41 P AP TP GP CP G 3" 2 $DNA__5__D__GP_GP_CP_TP_AP__T41_P_AP_TP_GP_CP_G__3__ B . no . . . . . . rr_214d 1 

   stop_

save_


save_DNA__5__D__CP_GP_CP_AP_TP_AP_TP_AP_GP_CP_C__3__
   _Entity.Sf_category                       entity
   _Entity.Sf_framecode                      DNA__5__D__CP_GP_CP_AP_TP_AP_TP_AP_GP_CP_C__3__
   _Entity.Entry_ID                          rr_214d
   _Entity.ID                                1
   _Entity.Name                              DNA__5__D__CP_GP_CP_AP_TP_AP_TP_AP_GP_CP_C__3__
   _Entity.Type                              polymer
   _Entity.Polymer_type                      polydeoxyribonucleotide
   _Entity.Polymer_strand_ID                 A
   _Entity.Polymer_seq_one_letter_code       CGCATATAGCC
   _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                11
   _Entity.Paramagnetic                      no
   _Entity.Thiol_state                      "not present"
   _Entity.Parent_entity_ID                  1
   _Entity.Formula_weight                    3373.12366

   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_214d 1 
       2 . DG . rr_214d 1 
       3 . DC . rr_214d 1 
       4 . DA . rr_214d 1 
       5 . DT . rr_214d 1 
       6 . DA . rr_214d 1 
       7 . DT . rr_214d 1 
       8 . DA . rr_214d 1 
       9 . DG . rr_214d 1 
      10 . DC . rr_214d 1 
      11 . DC . rr_214d 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_214d 1 
      . DG  2  2 rr_214d 1 
      . DC  3  3 rr_214d 1 
      . DA  4  4 rr_214d 1 
      . DT  5  5 rr_214d 1 
      . DA  6  6 rr_214d 1 
      . DT  7  7 rr_214d 1 
      . DA  8  8 rr_214d 1 
      . DG  9  9 rr_214d 1 
      . DC 10 10 rr_214d 1 
      . DC 11 11 rr_214d 1 

   stop_

save_


save_DNA__5__D__GP_GP_CP_TP_AP__T41_P_AP_TP_GP_CP_G__3__
   _Entity.Sf_category                       entity
   _Entity.Sf_framecode                      DNA__5__D__GP_GP_CP_TP_AP__T41_P_AP_TP_GP_CP_G__3__
   _Entity.Entry_ID                          rr_214d
   _Entity.ID                                2
   _Entity.Name                              DNA__5__D__GP_GP_CP_TP_AP__T41_P_AP_TP_GP_CP_G__3__
   _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                11
   _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_214d 2 
       2 . DG  . rr_214d 2 
       3 . DC  . rr_214d 2 
       4 . DT  . rr_214d 2 
       5 . DA  . rr_214d 2 
       6 . T41 . rr_214d 2 
       7 . DA  . rr_214d 2 
       8 . DT  . rr_214d 2 
       9 . DG  . rr_214d 2 
      10 . DC  . rr_214d 2 
      11 . DG  . rr_214d 2 

   stop_

save_


save_chem_comp_T41
   _Chem_comp.Sf_category      chem_comp
   _Chem_comp.Sf_framecode     chem_comp_T41
   _Chem_comp.Entry_ID         rr_214d
   _Chem_comp.ID               T41
   _Chem_comp.Name            "1-(2-O-METHYL-BETA-D-ARABINOFURANOSYL)THYMIDINE 5'-MONOPHOSPHATE"
   _Chem_comp.Type             non-polymer
   _Chem_comp.PDB_code         T41
   _Chem_comp.Formal_charge    0
   _Chem_comp.Paramagnetic     no
   _Chem_comp.Aromatic         no
   _Chem_comp.Formula         "C11 H17 N2 O9 P"
   _Chem_comp.Formula_weight   352.23706

save_


save_conformer_statistics
   _Conformer_stat_list.Sf_category                     conformer_statistics
   _Conformer_stat_list.Sf_framecode                    conformer_statistics
   _Conformer_stat_list.Entry_ID                        rr_214d
   _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_214d
   _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 214d.mr . . "MR format" 1  comment               "Not applicable" "Not applicable" 0 rr_214d 1 
      1 214d.mr . . "MR format" 2  distance               NOE              simple          0 rr_214d 1 
      1 214d.mr . . "MR format" 3 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_214d 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_214d
   _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 07-JUL-95 214D *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: DNA DUPLEX (MODIFIED) *COMPND 3 (5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*GP*CP*C)-3') (DOT) *COMPND 4 (5'-D(*GP*GP*CP*TP*AP*XP*AP*TP*GP*CP*G)-3') WHERE X IS *COMPND 5 1-(2-O-METHYL-BETA-D-ARABINOFURANOSYL)THYMIDINE; *COMPND 6 CHAIN: A, B; *COMPND 7 SYNONYM: 2'-OCH3-ARAT DNA, TAXA; *COMPND 8 ENGINEERED: YES *SOURCE MOL_ID: 1; *SOURCE 2 SYNTHETIC: YES *EXPDTA NMR, 40 STRUCTURES *AUTHOR C.H.GOTFREDSEN,H.P.SPIELMANN,J.WENGEL,J.P.JACOBSEN *REVDAT 1 15-OCT-95 214D 0 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 0.65 % of the REMARK largest integrated cross peak. 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 bounds for The correlation REMARK time used in the relaxation matrix calculations was 2.0ns.
REMARK REMARK
REMARK LOWER UPPER
REMARK ATOM 1 ATOM 2 BOUND BOUND
;

save_

