data_wwPDB_remediated_restraints_file_for_PDB_entry_1pdc

# This wwPDB archive file contains, for PDB entry 1pdc:
#
# - 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_1pdc
   _Entry.Title                        "wwPDB remediated NMR restraints for PDB entry 1pdc"
   _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 1pdc"

save_


save_assembly
   _Assembly.Sf_category            assembly
   _Assembly.Sf_framecode           assembly
   _Assembly.Entry_ID               rr_1pdc
   _Assembly.ID                     1
   _Assembly.Name                   1pdc
   _Assembly.Number_of_components   1
   _Assembly.Organic_ligands        0
   _Assembly.Metal_ions             0
   _Assembly.Non_standard_bonds     no
   _Assembly.Paramagnetic           no
   _Assembly.Thiol_state           "all free"
   _Assembly.Molecular_mass         5371.2037

   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 "SEMINAL FLUID PROTEIN PDC 109" 1 $SEMINAL_FLUID_PROTEIN_PDC_109 A . no . . . . . . rr_1pdc 1 

   stop_

save_


save_SEMINAL_FLUID_PROTEIN_PDC_109
   _Entity.Sf_category                       entity
   _Entity.Sf_framecode                      SEMINAL_FLUID_PROTEIN_PDC_109
   _Entity.Entry_ID                          rr_1pdc
   _Entity.ID                                1
   _Entity.Name                              SEMINAL_FLUID_PROTEIN_PDC_109
   _Entity.Type                              polymer
   _Entity.Polymer_type                      polypeptide(L)
   _Entity.Polymer_strand_ID                 A
   _Entity.Polymer_seq_one_letter_code      
;
DYAKCVFPFIYGGKKYETCT
KIGSMWMSWCSLSPNYDKDR
AWKYC
;
   _Entity.Ambiguous_conformational_states   no
   _Entity.Ambiguous_chem_comp_sites         no
   _Entity.Nstd_monomer                      no
   _Entity.Nstd_chirality                    no
   _Entity.Nstd_linkage                      no
   _Entity.Number_of_monomers                45
   _Entity.Paramagnetic                      no
   _Entity.Thiol_state                      "all free"
   _Entity.Parent_entity_ID                  1
   _Entity.Formula_weight                    5371.2037

   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 . ASP . rr_1pdc 1 
       2 . TYR . rr_1pdc 1 
       3 . ALA . rr_1pdc 1 
       4 . LYS . rr_1pdc 1 
       5 . CYS . rr_1pdc 1 
       6 . VAL . rr_1pdc 1 
       7 . PHE . rr_1pdc 1 
       8 . PRO . rr_1pdc 1 
       9 . PHE . rr_1pdc 1 
      10 . ILE . rr_1pdc 1 
      11 . TYR . rr_1pdc 1 
      12 . GLY . rr_1pdc 1 
      13 . GLY . rr_1pdc 1 
      14 . LYS . rr_1pdc 1 
      15 . LYS . rr_1pdc 1 
      16 . TYR . rr_1pdc 1 
      17 . GLU . rr_1pdc 1 
      18 . THR . rr_1pdc 1 
      19 . CYS . rr_1pdc 1 
      20 . THR . rr_1pdc 1 
      21 . LYS . rr_1pdc 1 
      22 . ILE . rr_1pdc 1 
      23 . GLY . rr_1pdc 1 
      24 . SER . rr_1pdc 1 
      25 . MET . rr_1pdc 1 
      26 . TRP . rr_1pdc 1 
      27 . MET . rr_1pdc 1 
      28 . SER . rr_1pdc 1 
      29 . TRP . rr_1pdc 1 
      30 . CYS . rr_1pdc 1 
      31 . SER . rr_1pdc 1 
      32 . LEU . rr_1pdc 1 
      33 . SER . rr_1pdc 1 
      34 . PRO . rr_1pdc 1 
      35 . ASN . rr_1pdc 1 
      36 . TYR . rr_1pdc 1 
      37 . ASP . rr_1pdc 1 
      38 . LYS . rr_1pdc 1 
      39 . ASP . rr_1pdc 1 
      40 . ARG . rr_1pdc 1 
      41 . ALA . rr_1pdc 1 
      42 . TRP . rr_1pdc 1 
      43 . LYS . rr_1pdc 1 
      44 . TYR . rr_1pdc 1 
      45 . CYS . rr_1pdc 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

      . ASP  1  1 rr_1pdc 1 
      . TYR  2  2 rr_1pdc 1 
      . ALA  3  3 rr_1pdc 1 
      . LYS  4  4 rr_1pdc 1 
      . CYS  5  5 rr_1pdc 1 
      . VAL  6  6 rr_1pdc 1 
      . PHE  7  7 rr_1pdc 1 
      . PRO  8  8 rr_1pdc 1 
      . PHE  9  9 rr_1pdc 1 
      . ILE 10 10 rr_1pdc 1 
      . TYR 11 11 rr_1pdc 1 
      . GLY 12 12 rr_1pdc 1 
      . GLY 13 13 rr_1pdc 1 
      . LYS 14 14 rr_1pdc 1 
      . LYS 15 15 rr_1pdc 1 
      . TYR 16 16 rr_1pdc 1 
      . GLU 17 17 rr_1pdc 1 
      . THR 18 18 rr_1pdc 1 
      . CYS 19 19 rr_1pdc 1 
      . THR 20 20 rr_1pdc 1 
      . LYS 21 21 rr_1pdc 1 
      . ILE 22 22 rr_1pdc 1 
      . GLY 23 23 rr_1pdc 1 
      . SER 24 24 rr_1pdc 1 
      . MET 25 25 rr_1pdc 1 
      . TRP 26 26 rr_1pdc 1 
      . MET 27 27 rr_1pdc 1 
      . SER 28 28 rr_1pdc 1 
      . TRP 29 29 rr_1pdc 1 
      . CYS 30 30 rr_1pdc 1 
      . SER 31 31 rr_1pdc 1 
      . LEU 32 32 rr_1pdc 1 
      . SER 33 33 rr_1pdc 1 
      . PRO 34 34 rr_1pdc 1 
      . ASN 35 35 rr_1pdc 1 
      . TYR 36 36 rr_1pdc 1 
      . ASP 37 37 rr_1pdc 1 
      . LYS 38 38 rr_1pdc 1 
      . ASP 39 39 rr_1pdc 1 
      . ARG 40 40 rr_1pdc 1 
      . ALA 41 41 rr_1pdc 1 
      . TRP 42 42 rr_1pdc 1 
      . LYS 43 43 rr_1pdc 1 
      . TYR 44 44 rr_1pdc 1 
      . CYS 45 45 rr_1pdc 1 

   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_1pdc
   _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_1pdc
   _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 1pdc.mr . . "MR format" 1  comment               "Not applicable" "Not applicable" 0 rr_1pdc 1 
      1 1pdc.mr . .  n/a        2  comment               "Not applicable" "Not applicable" 0 rr_1pdc 1 
      1 1pdc.mr . .  unknown    3 "dihedral angle"       "Not applicable" "Not applicable" 0 rr_1pdc 1 
      1 1pdc.mr . .  n/a        4  comment               "Not applicable" "Not applicable" 0 rr_1pdc 1 
      1 1pdc.mr . .  unknown    5  distance               NOE              simple          0 rr_1pdc 1 
      1 1pdc.mr . .  n/a        6  comment               "Not applicable" "Not applicable" 0 rr_1pdc 1 
      1 1pdc.mr . . "MR format" 7 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_1pdc 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_1pdc
   _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 COLLAGEN-BINDING TYPE II DOMAIN 10-OCT-91 1PDC *COMPND SEMINAL FLUID PROTEIN PDC-109 (DOMAIN B) *COMPND 2 (NMR, BEST STRUCTURE) *SOURCE BOVINE (BOS TAURUS) SEMINAL FLUID *AUTHOR M.LLINAS,K.L.CONSTANTINE,L.PATTHY *REVDAT 1 31-JAN-94 1PDC 0 Refined Solution Structure and Ligand-Binding Properties of PDC-109 Domain b, a Collagen-Binding Type II Domain Supplementary Material 
;

save_


save_MR_file_comment_4
   _Org_constr_file_comment.Sf_framecode         MR_file_comment_4
   _Org_constr_file_comment.Sf_category          org_constr_file_comment
   _Org_constr_file_comment.Entry_ID             rr_1pdc
   _Org_constr_file_comment.ID                   3
   _Org_constr_file_comment.Constraint_file_ID   1
   _Org_constr_file_comment.Block_ID             4
   _Org_constr_file_comment.Details             "Generated by Wattos"
   _Org_constr_file_comment.Comment             
;
 Table S2 Distance Constraints Used in PDC-109/b XPLOR Computations __________________________________________________________________ upper bounds (A) ___________________ refined estimated
residue 1 atom 1 residue 2 atom 2 set set 
;

save_


save_MR_file_comment_2
   _Org_constr_file_comment.Sf_framecode         MR_file_comment_2
   _Org_constr_file_comment.Sf_category          org_constr_file_comment
   _Org_constr_file_comment.Entry_ID             rr_1pdc
   _Org_constr_file_comment.ID                   2
   _Org_constr_file_comment.Constraint_file_ID   1
   _Org_constr_file_comment.Block_ID             2
   _Org_constr_file_comment.Details             "Generated by Wattos"
   _Org_constr_file_comment.Comment             
;
 Table S1 PDC-109/b Dihedral Angle Constraints __________________________________________________________________ dihedral angle (deg) residue PHI CHI1
__________________________________________________________________
;

save_


save_MR_file_comment_6
   _Org_constr_file_comment.Sf_framecode         MR_file_comment_6
   _Org_constr_file_comment.Sf_category          org_constr_file_comment
   _Org_constr_file_comment.Entry_ID             rr_1pdc
   _Org_constr_file_comment.ID                   4
   _Org_constr_file_comment.Constraint_file_ID   1
   _Org_constr_file_comment.Block_ID             6
   _Org_constr_file_comment.Details             "Generated by Wattos"
   _Org_constr_file_comment.Comment             
;
 Atom names refer to XPLOR [Brunger, A. T. (1990). X-PLOR (Version 2.1) Manual, Yale University Press] notation. An asterisk (*) following an atom name indicates that r to the -6 averaging was used for the equivalent or non-stereospecifically assigned proton pair.
The third set of constraints consists of max(refined,estimated) distances.
Distances were refined using the MIDGE program [Madrid, M., Llinas, E. & Llinas, M. (1990). J. Mag. Reson., in press.] 
;

save_

