data_wwPDB_remediated_restraints_file_for_PDB_entry_1d20

# This wwPDB archive file contains, for PDB entry 1d20:
#
# - 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_1d20
   _Entry.Title                        "wwPDB remediated NMR restraints for PDB entry 1d20"
   _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 1d20"

save_


save_assembly
   _Assembly.Sf_category            assembly
   _Assembly.Sf_framecode           assembly
   _Assembly.Entry_ID               rr_1d20
   _Assembly.ID                     1
   _Assembly.Name                   1d20
   _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         6200.906

   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 TP CP TP AP TP CP AP CP CP G 3" 1 $DNA__5__D__TP_CP_TP_AP_TP_CP_AP_CP_CP_G__3__ A . no . . . . . . rr_1d20 1 
      2 "DNA 5 D CP GP GP TP GP AP TP AP GP A 3" 2 $DNA__5__D__CP_GP_GP_TP_GP_AP_TP_AP_GP_A__3__ B . no . . . . . . rr_1d20 1 

   stop_

save_


save_DNA__5__D__TP_CP_TP_AP_TP_CP_AP_CP_CP_G__3__
   _Entity.Sf_category                       entity
   _Entity.Sf_framecode                      DNA__5__D__TP_CP_TP_AP_TP_CP_AP_CP_CP_G__3__
   _Entity.Entry_ID                          rr_1d20
   _Entity.ID                                1
   _Entity.Name                              DNA__5__D__TP_CP_TP_AP_TP_CP_AP_CP_CP_G__3__
   _Entity.Type                              polymer
   _Entity.Polymer_type                      polydeoxyribonucleotide
   _Entity.Polymer_strand_ID                 A
   _Entity.Polymer_seq_one_letter_code       TCTATCACCG
   _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                10
   _Entity.Paramagnetic                      no
   _Entity.Thiol_state                      "not present"
   _Entity.Parent_entity_ID                  1
   _Entity.Formula_weight                    3035.9097

   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 . DT . rr_1d20 1 
       2 . DC . rr_1d20 1 
       3 . DT . rr_1d20 1 
       4 . DA . rr_1d20 1 
       5 . DT . rr_1d20 1 
       6 . DC . rr_1d20 1 
       7 . DA . rr_1d20 1 
       8 . DC . rr_1d20 1 
       9 . DC . rr_1d20 1 
      10 . DG . rr_1d20 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

      . DT  1  1 rr_1d20 1 
      . DC  2  2 rr_1d20 1 
      . DT  3  3 rr_1d20 1 
      . DA  4  4 rr_1d20 1 
      . DT  5  5 rr_1d20 1 
      . DC  6  6 rr_1d20 1 
      . DA  7  7 rr_1d20 1 
      . DC  8  8 rr_1d20 1 
      . DC  9  9 rr_1d20 1 
      . DG 10 10 rr_1d20 1 

   stop_

save_


save_DNA__5__D__CP_GP_GP_TP_GP_AP_TP_AP_GP_A__3__
   _Entity.Sf_category                       entity
   _Entity.Sf_framecode                      DNA__5__D__CP_GP_GP_TP_GP_AP_TP_AP_GP_A__3__
   _Entity.Entry_ID                          rr_1d20
   _Entity.ID                                2
   _Entity.Name                              DNA__5__D__CP_GP_GP_TP_GP_AP_TP_AP_GP_A__3__
   _Entity.Type                              polymer
   _Entity.Polymer_type                      polydeoxyribonucleotide
   _Entity.Polymer_strand_ID                 B
   _Entity.Polymer_seq_one_letter_code       CGGTGATAGA
   _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                10
   _Entity.Paramagnetic                      no
   _Entity.Thiol_state                      "not present"
   _Entity.Parent_entity_ID                  2
   _Entity.Formula_weight                    3164.9963

   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_1d20 2 
       2 . DG . rr_1d20 2 
       3 . DG . rr_1d20 2 
       4 . DT . rr_1d20 2 
       5 . DG . rr_1d20 2 
       6 . DA . rr_1d20 2 
       7 . DT . rr_1d20 2 
       8 . DA . rr_1d20 2 
       9 . DG . rr_1d20 2 
      10 . DA . rr_1d20 2 

   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_1d20 2 
      . DG  2  2 rr_1d20 2 
      . DG  3  3 rr_1d20 2 
      . DT  4  4 rr_1d20 2 
      . DG  5  5 rr_1d20 2 
      . DA  6  6 rr_1d20 2 
      . DT  7  7 rr_1d20 2 
      . DA  8  8 rr_1d20 2 
      . DG  9  9 rr_1d20 2 
      . DA 10 10 rr_1d20 2 

   stop_

save_


save_conformer_statistics
   _Conformer_stat_list.Sf_category                     conformer_statistics
   _Conformer_stat_list.Sf_framecode                    conformer_statistics
   _Conformer_stat_list.Entry_ID                        rr_1d20
   _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_1d20
   _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 1d20.mr . . "MR format"  1  comment               "Not applicable"   "Not applicable" 0 rr_1d20 1 
      1 1d20.mr . .  unknown     2  distance               NOE                simple          0 rr_1d20 1 
      1 1d20.mr . .  n/a         3  comment               "Not applicable"   "Not applicable" 0 rr_1d20 1 
      1 1d20.mr . .  unknown     4  distance               NOE                simple          0 rr_1d20 1 
      1 1d20.mr . .  n/a         5  comment               "Not applicable"   "Not applicable" 0 rr_1d20 1 
      1 1d20.mr . .  unknown     6  distance               NOE                simple          0 rr_1d20 1 
      1 1d20.mr . .  n/a         7  comment               "Not applicable"   "Not applicable" 0 rr_1d20 1 
      1 1d20.mr . .  unknown     8  distance               NOE                simple          0 rr_1d20 1 
      1 1d20.mr . .  n/a         9  comment               "Not applicable"   "Not applicable" 0 rr_1d20 1 
      1 1d20.mr . .  unknown    10 "dihedral angle"       "Not applicable"   "Not applicable" 0 rr_1d20 1 
      1 1d20.mr . .  n/a        11  comment               "Not applicable"   "Not applicable" 0 rr_1d20 1 
      1 1d20.mr . .  unknown    12  distance              "general distance"  simple          0 rr_1d20 1 
      1 1d20.mr . .  n/a        13  comment               "Not applicable"   "Not applicable" 0 rr_1d20 1 
      1 1d20.mr . . "MR format" 14 "nomenclature mapping" "Not applicable"   "Not applicable" 0 rr_1d20 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_1d20
   _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 R1D20MR 01-AUG-90
*COMPND /DNA$ (5'-$D(*TP*CP*TP*AP*TP*CP*AP*CP*CP*GP)-3') *SOURCE SYNTHETIC /DNA$ *EXPDTA NMR *AUTHOR J.D.BALEJA,B.D.SYKES *COORDS 1D20
*REMARK *REMARK HYDROGEN ATOMS IN THIS ENTRY HAVE BEEN ASSIGNED NAMES *REMARK CONSISTENT WITH THE RECOMMENDATIONS OF THE IUPAC-IUB *REMARK COMMISSION ON BIOCHEMICAL NOMENCLATURE (SEE,E.G., J.MOL. *REMARK BIOL. 52, 1 (1970)). THE PROTEIN DATA BANK HAS FOLLOWED *REMARK RULE 4.4 OF THE RECOMMENDATIONS WITH THE FOLLOWING *REMARK MODIFICATION - WHEN MORE THAN ONE HYDROGEN ATOM IS BONDED *REMARK TO A SINGLE NON-HYDROGEN ATOM, THE HYDROGEN ATOM NUMBER *REMARK DESIGNATION IS GIVEN AS THE FIRST CHARACTER OF THE ATOM *REMARK NAME RATHER THAN AS THE LAST CHARACTER (E.G. H*BETA*1 IS *REMARK DENOTED AS 1HB). *REMARK File 9. Experimental restraints for L10 DNAa A. NOE intensities and distances in D2O Mixing time (sec.) Distance estimate Proton Pair (nm.) 0.050 0.100 0.150 0.250 Lower Upper 1. Resolved cross-peaks 
;

save_


save_MR_file_comment_5
   _Org_constr_file_comment.Sf_framecode         MR_file_comment_5
   _Org_constr_file_comment.Sf_category          org_constr_file_comment
   _Org_constr_file_comment.Entry_ID             rr_1d20
   _Org_constr_file_comment.ID                   3
   _Org_constr_file_comment.Constraint_file_ID   1
   _Org_constr_file_comment.Block_ID             5
   _Org_constr_file_comment.Details             "Generated by Wattos"
   _Org_constr_file_comment.Comment             
;
3. Covalently bound proton pairs 
;

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_1d20
   _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             
;
2. Overlapping cross-peaks 
;

save_


save_MR_file_comment_9
   _Org_constr_file_comment.Sf_framecode         MR_file_comment_9
   _Org_constr_file_comment.Sf_category          org_constr_file_comment
   _Org_constr_file_comment.Entry_ID             rr_1d20
   _Org_constr_file_comment.ID                   5
   _Org_constr_file_comment.Constraint_file_ID   1
   _Org_constr_file_comment.Block_ID             9
   _Org_constr_file_comment.Details             "Generated by Wattos"
   _Org_constr_file_comment.Comment             
;
C. Dihedral Angle restraints (upper and lower bounds) 
;

save_


save_MR_file_comment_7
   _Org_constr_file_comment.Sf_framecode         MR_file_comment_7
   _Org_constr_file_comment.Sf_category          org_constr_file_comment
   _Org_constr_file_comment.Entry_ID             rr_1d20
   _Org_constr_file_comment.ID                   4
   _Org_constr_file_comment.Constraint_file_ID   1
   _Org_constr_file_comment.Block_ID             7
   _Org_constr_file_comment.Details             "Generated by Wattos"
   _Org_constr_file_comment.Comment             
;
B. NOE intensities and distances for exchangeable protons e NOE intensities Distance (nm.) Proton pair .1 .2 .3 .5 sec. 
;

save_


save_MR_file_comment_13
   _Org_constr_file_comment.Sf_framecode         MR_file_comment_13
   _Org_constr_file_comment.Sf_category          org_constr_file_comment
   _Org_constr_file_comment.Entry_ID             rr_1d20
   _Org_constr_file_comment.ID                   7
   _Org_constr_file_comment.Constraint_file_ID   1
   _Org_constr_file_comment.Block_ID             13
   _Org_constr_file_comment.Details             "Generated by Wattos"
   _Org_constr_file_comment.Comment             
;
aThe absence of an entry indicates that no distance estimate was made, or that the NOE intensity was not tabulated. NOE intensities and distances were not used for 5' and 5" protons because they were not assigned stereospecifically, and because the ratio of J5'5" to the difference in chemical shifts is often not small, leading to second order effects.
bNOE noted in subsequent analysis of the data, but not used in structure refinement.
cNOE and distances are included with the previous entry.
dNOE and distances are approximately equal to the previous entry.
eThe one-dimensional difference NOEs are in percentage of the height of the irradiated imino peak. Imino-imino(i,j) NOE intensities are an average of the NOE observed on j while irradiating i, and the NOE observed on i, when irradiating j.
fwhere applicable. For example, residue 1 has no 5' phosphate, and therefore, no corresponding alpha angle. *REMARK
*REMARK THE FOLLOWING IS A LIST OF ALL HYDROGEN ATOMS WITH THEIR *REMARK NAMES IN THE ENTRY AND THE ORIGINAL DATA:
;

save_


save_MR_file_comment_11
   _Org_constr_file_comment.Sf_framecode         MR_file_comment_11
   _Org_constr_file_comment.Sf_category          org_constr_file_comment
   _Org_constr_file_comment.Entry_ID             rr_1d20
   _Org_constr_file_comment.ID                   6
   _Org_constr_file_comment.Constraint_file_ID   1
   _Org_constr_file_comment.Block_ID             11
   _Org_constr_file_comment.Details             "Generated by Wattos"
   _Org_constr_file_comment.Comment             
;
D. Major Groove distance restraints (nm.) 
;

save_

