data_20084 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DIRHODIUM PEPTIDE COMPLEX ; _BMRB_accession_number 20084 _BMRB_flat_file_name bmr20084.str _Entry_type new _Submission_date 2009-07-14 _Accession_date 2009-07-14 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; NMR SOLUTION STRUCTURE OF THE DIRHODIUM COMPLEX WITH A PEPTIDE DERIVED FROM ZINC FINGER PROTEIN The protein in the PDB file includes two chemical components, RH3 and ACT. In the NMR-STAR file, it includes one, DRA. The PDB file includes the source organism although the NMR-STAR file has no natural source. The best representative conformer 4 was moved to MODEL 1. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zaykov Alexander N. . 2 Ball Zach T. . 3 MacKenzie Kevin R. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 80 "13C chemical shifts" 44 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-02-10 update BMRB 'PDBj annotated the coordinate file' 2010-03-01 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Controlling peptide structure with coordination chemistry: robust and reversible peptide-dirhodium ligation.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19637261 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zaykov Alexander N. . 2 MacKenzie Kevin R. . 3 Ball Zachary T. . stop_ _Journal_abbreviation 'Chem.--Eur. J.' _Journal_name_full 'Chemistry--A European Journal' _Journal_volume 15 _Journal_issue 36 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8961 _Page_last 8965 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Dirhodium complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Peptide $Zinc_Finger_Based_Peptide 'Rhodium, 1' $RH3 'Rhodium, 2' $RH3 'ACETATE ION, 1' $ACT 'ACETATE ION, 2' $ACT stop_ _System_molecular_weight . _System_physical_state unfolded _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Zinc_Finger_Based_Peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Zinc_Finger_Based_Peptide _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence PFADSIDGRKFAX loop_ _Residue_seq_code _Residue_label 1 PRO 2 PHE 3 ALA 4 ASP 5 SER 6 ILE 7 ASP 8 GLY 9 ARG 10 LYS 11 PHE 12 ALA 13 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'AMINO GROUP' _BMRB_code . _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Feb 10 16:32:38 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N HN1 ? ? SING N HN2 ? ? stop_ save_ ############# # Ligands # ############# save_RH3 _Saveframe_category ligand _Mol_type non-polymer _Name_common "RH3 (RHODIUM(III) ION)" _BMRB_code . _PDB_code RH3 _Molecular_mass 102.906 _Mol_charge 3 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Feb 10 16:29:34 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons RH RH RH . 3 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ save_ACT _Saveframe_category ligand _Mol_type non-polymer _Name_common "ACT (ACETATE ION)" _BMRB_code . _PDB_code ACT _Molecular_mass 59.044 _Mol_charge -1 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Feb 10 16:33:54 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? OXT OXT O . -1 . ? CH3 CH3 C . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB C O ? ? SING C OXT ? ? SING C CH3 ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Deleted_atom_mol_system_component_name _Deleted_atom_residue_seq_code _Deleted_atom_residue_label _Deleted_atom_name Peptide 4 ASP HG Peptide 7 ASP HG stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Zinc_Finger_Based_Peptide . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $Zinc_Finger_Based_Peptide 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Zinc_Finger_Based_Peptide 6 mM 'natural abundance' 'sodium acetate' 0.23 M 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' $RH3 12 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' 'chemical shift assignment' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_WROESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H WROESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 293 . K pH 5.5 . pH stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio water H 1 protons ppm 4.8 internal direct . . . 1.000000000 water C 13 protons ppm 0 external indirect . . . 0.251449530 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-1H COSY' '2D 1H-1H WROESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name Peptide _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 PRO HA H 4.319 0.005 4 2 1 1 PRO HB2 H 2.018 0.003 1 3 1 1 PRO HB3 H 2.431 0.003 1 4 1 1 PRO HD2 H 3.368 0.001 1 5 1 1 PRO HD3 H 3.408 0.000 1 6 1 1 PRO HG2 H 2.023 0.003 1 7 1 1 PRO HG3 H 2.023 0.003 1 8 1 1 PRO CA C 62.422 0.000 1 9 1 1 PRO CB C 32.568 0.000 1 10 1 1 PRO CD C 49.482 0.000 1 11 1 1 PRO CG C 26.537 0.000 1 12 2 2 PHE H H 8.725 0.002 1 13 2 2 PHE HA H 4.678 0.004 1 14 2 2 PHE HB2 H 3.044 0.003 1 15 2 2 PHE HB3 H 3.118 0.004 1 16 2 2 PHE HD1 H 7.258 0.003 3 17 2 2 PHE HD2 H 7.258 0.003 3 18 2 2 PHE HZ H 7.303 0.000 5 19 2 2 PHE CA C 57.945 0.000 1 20 2 2 PHE CB C 39.727 0.000 1 21 2 2 PHE CD1 C 132.022 0.000 5 22 2 2 PHE CD2 C 132.022 0.000 5 23 2 2 PHE CE1 C 131.533 0.000 5 24 2 2 PHE CE2 C 131.533 0.000 5 25 2 2 PHE CZ C 130.002 0.000 5 26 3 3 ALA H H 8.489 0.001 1 27 3 3 ALA HA H 4.279 0.005 4 28 3 3 ALA HB H 1.331 0.003 4 29 3 3 ALA CA C 52.733 0.000 1 30 3 3 ALA CB C 18.91 0.000 1 31 4 4 ASP H H 8.275 0.002 1 32 4 4 ASP HA H 4.739 0.004 1 33 4 4 ASP HB2 H 2.693 0.004 4 34 4 4 ASP HB3 H 2.435 0.003 1 35 4 4 ASP CA C 57.57 0.000 1 36 4 4 ASP CB C 40.022 0.000 1 37 5 5 SER H H 8.056 0.001 1 38 5 5 SER HA H 4.1 0.003 4 39 5 5 SER HB2 H 3.843 0.004 1 40 5 5 SER HB3 H 3.913 0.005 1 41 5 5 SER CA C 62.148 0.000 1 42 5 5 SER CB C 63.031 0.000 1 43 6 6 ILE H H 7.869 0.004 4 44 6 6 ILE HA H 4.101 0.002 4 45 6 6 ILE HB H 2.034 0.005 1 46 6 6 ILE HD1 H 0.997 0.003 1 47 6 6 ILE HG12 H 1.028 0.002 1 48 6 6 ILE HG13 H 1.028 0.002 1 49 6 6 ILE HG2 H 1.53 0.004 1 50 6 6 ILE CA C 60.584 0.000 1 51 6 6 ILE CB C 38.149 0.000 1 52 6 6 ILE CD1 C 13.929 0.000 1 53 6 6 ILE CG1 C 18.123 0.000 1 54 6 6 ILE CG2 C 28.095 0.000 1 55 7 7 ASP H H 7.351 0.001 1 56 7 7 ASP HA H 4.327 0.003 4 57 7 7 ASP HB2 H 2.691 0.000 4 58 7 7 ASP HB3 H 2.739 0.008 4 59 7 7 ASP CA C 54.567 0.000 1 60 7 7 ASP CB C 39.472 0.000 1 61 8 8 GLY H H 7.973 0.002 1 62 8 8 GLY HA2 H 3.864 0.002 1 63 8 8 GLY HA3 H 3.953 0.005 1 64 8 8 GLY CA C 45.547 0.000 1 65 9 9 ARG H H 7.883 0.002 4 66 9 9 ARG HA H 4.278 0.004 4 67 9 9 ARG HB2 H 1.746 0.007 2 68 9 9 ARG HB3 H 1.803 0.004 2 69 9 9 ARG HD2 H 3.158 0.003 1 70 9 9 ARG HD3 H 3.158 0.003 1 71 9 9 ARG HG2 H 1.574 0.007 1 72 9 9 ARG HG3 H 1.574 0.007 1 73 9 9 ARG HH11 H 7.022 0.004 1 74 9 9 ARG HH12 H 7.022 0.004 1 75 9 9 ARG HH21 H 6.975 0.004 1 76 9 9 ARG HH22 H 6.975 0.004 1 77 9 9 ARG CA C 56.257 0.000 1 78 9 9 ARG CB C 30.797 0.000 1 79 9 9 ARG CD C 43.512 0.000 1 80 9 9 ARG CG C 27.055 0.000 1 81 10 10 LYS H H 8.213 0.002 4 82 10 10 LYS HA H 4.243 0.003 4 83 10 10 LYS HB2 H 1.666 0.002 1 84 10 10 LYS HB3 H 1.666 0.002 1 85 10 10 LYS HD2 H 1.619 0.002 1 86 10 10 LYS HD3 H 1.619 0.002 1 87 10 10 LYS HE2 H 2.95 0.010 1 88 10 10 LYS HE3 H 2.95 0.010 1 89 10 10 LYS HG2 H 1.265 0.007 1 90 10 10 LYS HG3 H 1.332 0.006 4 91 10 10 LYS HZ H 7.507 0.004 1 92 10 10 LYS CA C 56.457 0.000 1 93 10 10 LYS CB C 33.098 0.000 1 94 10 10 LYS CD C 29.089 0.000 1 95 10 10 LYS CE C 42.221 0.000 1 96 10 10 LYS CG C 24.724 0.000 1 97 11 11 PHE H H 8.239 0.004 1 98 11 11 PHE HA H 4.612 0.003 1 99 11 11 PHE HB2 H 3.014 0.002 1 100 11 11 PHE HB3 H 3.15 0.007 1 101 11 11 PHE HD1 H 7.263 0.001 3 102 11 11 PHE HD2 H 7.263 0.001 3 103 11 11 PHE HE1 H 7.309 0.001 3 104 11 11 PHE HE2 H 7.309 0.001 3 105 11 11 PHE HZ H 7.303 0.000 5 106 11 11 PHE CA C 57.654 0.000 1 107 11 11 PHE CD1 C 132.022 0.000 5 108 11 11 PHE CD2 C 132.022 0.000 5 109 11 11 PHE CE1 C 131.533 0.000 5 110 11 11 PHE CE2 C 131.533 0.000 5 111 11 11 PHE CZ C 130.002 0.000 5 112 12 12 ALA H H 8.209 0.004 4 113 12 12 ALA HA H 4.253 0.000 4 114 12 12 ALA HB H 1.34 0.002 4 115 12 12 ALA CA C 52.338 0.000 1 116 12 12 ALA CB C 19.568 0.000 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity ',,,' ',,,' ',' ',,,,,' ',,' ',' ',' stop_ save_ save_assigned_chem_shift_list_1_4 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-1H COSY' '2D 1H-1H WROESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'ACETATE ION, 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 ACT CH3 C 25.566 0.000 1 2 . 1 ACT H1 H 1.881 0.000 1 3 . 1 ACT H2 H 1.881 0.000 1 4 . 1 ACT H3 H 1.881 0.000 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity ',,,' ',,,' ',' ',,,,,' ',,' ',' ',' stop_ save_ save_assigned_chem_shift_list_1_5 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-1H COSY' '2D 1H-1H WROESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'ACETATE ION, 2' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 ACT CH3 C 25.566 0.000 1 2 . 1 ACT H1 H 1.888 0.000 1 3 . 1 ACT H2 H 1.888 0.000 1 4 . 1 ACT H3 H 1.888 0.000 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity ',,,' ',,,' ',' ',,,,,' ',,' ',' ',' stop_ save_ save_constraint_statistics _Saveframe_category constraint_statistics _Text_data_format . _Text_data . _NOE_interproton_distance_evaluation . _NOE_pseudoatom_corrections . _Details . save_