data_2217 #Corrected using PDB structure: 2EXFA # #N.B. (Observed* = Observed shift + Offset correction) # #After reference correction, the following residues still #have a HA chemical shift difference (obs*-pred) greater than 0.7ppm: #NUM AA CS Observed* Predicted # 34 M HA 4.68 3.95 # #The average CS difference between predicted and observed: #HA CA CB CO N HN #-0.15 N/A N/A N/A N/A -0.20 # #bmr2217.str.corr chemical shifts have been re-referenced with the following #offsets (these values have been added to the original bmr2217.str file): #HA CA CB CO N HN #N/A N/A N/A N/A N/A N/A # #The 95% confidence intervals for the above recommended offsets are: # HA CA CB CO N HN #+/-0.06 N/A N/A N/A N/A +/-0.16 # #The Correlation Coefficients between predicted and observed #chemical shifts are: #HA CA CB CO N HN #0.553 N/A N/A N/A N/A 0.354 # #The RMSD between predicted and observed* (reference #corrected) chemical shifts are: #HA CA CB CO N HN #0.181 N/A N/A N/A N/A 0.478 # ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Omichinski James G. . 2 Clore G. Marius . 3 Sakaguchi Kazuyasu . . 4 Appella Ettore . . 5 Gronenborn Angela M. . stop_ _BMRB_accession_number 2217 _BMRB_flat_file_name bmr2217.str _Entry_type revision _Submission_date 1995-07-31 _Accession_date 1996-03-25 _Entry_origination BMRB _NMR_STAR_version 2.1 _Experimental_method NMR loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count '1H chemical shifts' 241 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 1999-06-14 revision BMRB 'Converted to BMRB NMR-STAR V 2.1 format' 1996-03-25 reformat BMRB 'Converted to the BMRB 1996-03-01 STAR flat-file format' 1995-07-31 original BMRB 'Last release in original BMRB flat-file format' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Omichinski, James G., Clore, G. Marius, Sakaguchi, Kazuyasu, Appella, Ettore, Gronenborn, Angela M., "Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy," FEBS Lett. 292 (1-2), 25-30 (1991). ; _Citation_title ; Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy ; _Citation_status published _Citation_type journal _MEDLINE_UI_code ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Omichinski James G. . 2 Clore G. Marius . 3 Sakaguchi Kazuyasu . . 4 Appella Ettore . . 5 Gronenborn Angela M. . stop_ _Journal_abbreviation 'FEBS Lett.' _Journal_volume 292 _Journal_issue 1-2 _Page_first 25 _Page_last 30 _Year 1991 save_ ################################## # Molecular system description # ################################## save_system_nucleocapsid_protein _Saveframe_category molecular_system _Mol_system_name 'nucleocapsid protein' _Abbreviation_common ? loop_ _Mol_system_component_name _Mol_label 'nucleocapsid protein' $nucleocapsid_protein stop_ _System_physical_state ? _System_oligomer_state ? _System_paramagnetic ? loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Database_entry_details PDB 1BJ6 "A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES" . PDB 1ESK "A Chain A, Solution Structure Of Ncp7 From Hiv-1" . stop_ save_ ######################## # Monomeric polymers # ######################## save_nucleocapsid_protein _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'nucleocapsid protein' _Name_variant 'zinc finger domains p7-DF' _Abbreviation_common ? ############################## # Polymer residue sequence # ############################## _Residue_count 39 _Mol_residue_sequence ; VKCFNCGKEGHTARNCRAPR KKGCWKCGKEGHQMKDCTE ; loop_ _Residue_seq_code _Residue_label 1 VAL 2 LYS 3 CYS 4 PHE 5 ASN 6 CYS 7 GLY 8 LYS 9 GLU 10 GLY 11 HIS 12 THR 13 ALA 14 ARG 15 ASN 16 CYS 17 ARG 18 ALA 19 PRO 20 ARG 21 LYS 22 LYS 23 GLY 24 CYS 25 TRP 26 LYS 27 CYS 28 GLY 29 LYS 30 GLU 31 GLY 32 HIS 33 GLN 34 MET 35 LYS 36 ASP 37 CYS 38 THR 39 GLU stop_ _Sequence_homology_query_date 2004-07-29 _Sequence_homology_query_revised_last_date 2004-04-01 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 1BJ6 "A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC)COMPLEX, 10 STRUCTURES" 92.86 42 100 100 1e-19 PDB 1ESK "A Chain A, Solution Structure Of Ncp7 FromHiv-1" 92.86 42 100 100 1e-19 DBJ BAA12996.1 "Gag [Human immunodeficiency virus 1]" 7.62 512 100 100 1e-19 GenBank AAB21888.1 "nucleocapsid protein, NCp7, NC71 [humanimmunodeficiency virus type 1, HIV-1, PeptideRecombinant, 71 aa]" 54.93 71 100 100 1e-19 GenBank AAB50258.1 "gag polyprotein [Human immunodeficiencyvirus 1]" 7.80 500 100 100 1e-19 GenBank AAC82593.1 "Gag [Human immunodeficiency virus 1]" 7.80 500 100 100 1e-19 GenBank AAA44201.1 "gag polyprotein precursor" 7.62 512 100 100 1e-19 GenBank AAB59866.1 "gag polyprotein precursor [Humanimmunodeficiency virus type 1]" 7.62 512 100 100 1e-19 PIR FOVWVL "gag polyprotein - human immunodeficiency virustype 1 (isolate LV)" 8.16 478 100 100 1e-19 PIR FOVWH3 "gag polyprotein - human immunodeficiency virustype 1 (isolate HTLV-III, BH10)" 7.62 512 100 100 1e-19 PRF 1103299C "gag gene" 8.16 478 100 100 1e-19 PRF 1102247B "protein gag" 7.62 512 100 100 1e-19 REF NP_579881.1 "nucleocapsid [Human immunodeficiencyvirus 1]" 70.91 55 100 100 1e-19 REF NP_057850.1 "Gag [Human immunodeficiency virus 1]" 7.80 500 100 100 1e-19 REF NP_057849.4 "Gag-Pol; Gag-Pol polyprotein [Humanimmunodeficiency virus 1]" 2.72 1435 100 100 1e-19 SWISS-PROT P04591 "GAG_HV1H2 Gag polyprotein [Contains: Coreprotein p17 (Matrix protein); Core protein p24 (Coreantigen); Core protein p2; Core protein p7 (Nucleocapsidprotein); Core protein p1; Core protein p6]" 7.80 500 100 100 1e-19 SWISS-PROT P03347 "GAG_HV1B1 GAG polyprotein [Contains: Coreproteins P17, P24, P2, P7, P1, P6]" 7.62 512 100 100 1e-19 SWISS-PROT P03350 "GAG_HV1PV Gag polyprotein [Contains: Coreprotein p17 (Matrix protein); Core protein p24 (Coreantigen); Core protein p2; Core protein p7 (Nucleocapsidprotein); Core protein p1; Core protein p6]" 7.62 512 100 100 1e-19 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Genus _Strain $nucleocapsid_protein HIV ? HIV generic stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method $nucleocapsid_protein 'not available' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling ? ? ? ? stop_ save_ ####################### # Sample conditions # ####################### save_sample_condition_set_one _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.8 . na temperature 288 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_par_set_one _Saveframe_category chemical_shift_reference loop_ _Mol_common_name _Atom_type _Chem_shift_units _Chem_shift_value DSS H ppm 0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # Index Value Definition # # # # 1 Unique # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups # # 3 Aromatic atoms on opposite sides of the ring # # (e.g. Tyr HE1 and HE2 protons) # # 4 Intraresidue ambiguities (e.g. Lys HG and # # HD protons) # # 5 Interresidue ambiguities (Lys 12 vs. Lys 27) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_assignment_data_set_one _Saveframe_category assigned_chemical_shifts loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_condition_set_one _Chem_shift_reference_set_label $chem_shift_reference_par_set_one _Mol_system_component_name 'nucleocapsid protein' loop_ _Atom_shift_assign_ID _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 VAL HA H 3.77 . 1 2 1 VAL HB H 2.01 . 1 3 1 VAL HG1 H 0.83 . 1 4 1 VAL HG2 H 0.83 . 1 5 2 LYS H H 8.52 . 1 6 2 LYS HA H 4.41 . 1 7 2 LYS HB2 H 1.50 . 2 8 2 LYS HB3 H 1.44 . 2 9 2 LYS HG2 H 1.01 . 1 10 2 LYS HG3 H 1.01 . 1 11 2 LYS HD2 H 1.07 . 1 12 2 LYS HD3 H 1.07 . 1 13 2 LYS HE2 H 2.86 . 1 14 2 LYS HE3 H 2.86 . 1 15 3 CYS H H 8.31 . 1 16 3 CYS HA H 4.06 . 1 17 3 CYS HB2 H 2.78 . 2 18 3 CYS HB3 H 1.79 . 2 19 4 PHE H H 8.84 . 1 20 4 PHE HA H 4.47 . 1 21 4 PHE HB2 H 3.11 . 2 22 4 PHE HB3 H 3.22 . 2 23 4 PHE HD1 H 7.29 . 1 24 4 PHE HD2 H 7.29 . 1 25 4 PHE HE1 H 7.34 . 1 26 4 PHE HE2 H 7.34 . 1 27 4 PHE HZ H 7.34 . 1 28 5 ASN H H 9.56 . 1 29 5 ASN HA H 4.71 . 1 30 5 ASN HB2 H 2.75 . 2 31 5 ASN HB3 H 3.10 . 2 32 5 ASN HD21 H 6.83 . 2 33 5 ASN HD22 H 8.08 . 2 34 6 CYS H H 8.83 . 1 35 6 CYS HA H 4.91 . 1 36 6 CYS HB2 H 3.23 . 2 37 6 CYS HB3 H 2.48 . 2 38 7 GLY H H 7.94 . 1 39 7 GLY HA2 H 3.77 . 2 40 7 GLY HA3 H 4.09 . 2 41 8 LYS H H 8.14 . 1 42 8 LYS HA H 4.41 . 1 43 8 LYS HB2 H 1.87 . 2 44 8 LYS HB3 H 1.81 . 2 45 8 LYS HG2 H 1.72 . 1 46 8 LYS HG3 H 1.72 . 1 47 8 LYS HD2 H 1.50 . 1 48 8 LYS HD3 H 1.50 . 1 49 8 LYS HE2 H 3.02 . 1 50 8 LYS HE3 H 3.02 . 1 51 9 GLU H H 8.44 . 1 52 9 GLU HA H 4.52 . 1 53 9 GLU HB2 H 1.86 . 2 54 9 GLU HB3 H 2.11 . 2 55 9 GLU HG2 H 2.21 . 2 56 9 GLU HG3 H 2.37 . 2 57 10 GLY H H 8.56 . 1 58 10 GLY HA2 H 4.47 . 2 59 10 GLY HA3 H 3.74 . 2 60 11 HIS H H 7.22 . 1 61 11 HIS HA H 4.80 . 1 62 11 HIS HB2 H 3.21 . 1 63 11 HIS HB3 H 3.21 . 1 64 11 HIS HD2 H 7.06 . 1 65 11 HIS HE1 H 7.41 . 1 66 12 THR H H 8.27 . 1 67 12 THR HA H 4.68 . 1 68 12 THR HB H 4.48 . 1 69 12 THR HG2 H 1.15 . 1 70 13 ALA H H 8.93 . 1 71 13 ALA HA H 4.63 . 1 72 13 ALA HB H 1.43 . 1 73 14 ARG H H 8.11 . 1 74 14 ARG HA H 4.10 . 1 75 14 ARG HB2 H 1.69 . 2 76 14 ARG HB3 H 1.82 . 2 77 14 ARG HG2 H 1.61 . 1 78 14 ARG HG3 H 1.61 . 1 79 14 ARG HD2 H 3.16 . 1 80 14 ARG HD3 H 3.16 . 1 81 14 ARG HE H 7.21 . 1 82 15 ASN H H 7.93 . 1 83 15 ASN HA H 4.98 . 1 84 15 ASN HB2 H 2.58 . 2 85 15 ASN HB3 H 3.00 . 2 86 15 ASN HD21 H 6.93 . 2 87 15 ASN HD22 H 7.80 . 2 88 16 CYS H H 7.52 . 1 89 16 CYS HA H 3.86 . 1 90 16 CYS HB2 H 3.34 . 2 91 16 CYS HB3 H 2.95 . 2 92 17 ARG H H 8.36 . 1 93 17 ARG HA H 4.23 . 1 94 17 ARG HB2 H 1.74 . 2 95 17 ARG HB3 H 1.85 . 2 96 17 ARG HG2 H 1.64 . 1 97 17 ARG HG3 H 1.64 . 1 98 17 ARG HD2 H 3.12 . 1 99 17 ARG HD3 H 3.12 . 1 100 17 ARG HE H 7.20 . 1 101 18 ALA H H 8.26 . 1 102 18 ALA HA H 4.54 . 1 103 18 ALA HB H 1.30 . 1 104 19 PRO HA H 4.24 . 1 105 19 PRO HB2 H 1.78 . 2 106 19 PRO HB3 H 2.18 . 2 107 19 PRO HG2 H 1.93 . 1 108 19 PRO HG3 H 1.93 . 1 109 19 PRO HD2 H 3.54 . 2 110 19 PRO HD3 H 3.74 . 2 111 20 ARG H H 8.42 . 1 112 20 ARG HA H 4.25 . 1 113 20 ARG HB2 H 1.70 . 2 114 20 ARG HB3 H 1.78 . 2 115 20 ARG HG2 H 1.58 . 1 116 20 ARG HG3 H 1.58 . 1 117 20 ARG HD2 H 3.08 . 1 118 20 ARG HD3 H 3.08 . 1 119 20 ARG HE H 7.12 . 1 120 21 LYS H H 8.30 . 1 121 21 LYS HA H 4.24 . 1 122 21 LYS HB2 H 1.78 . 2 123 21 LYS HB3 H 1.69 . 2 124 21 LYS HG2 H 1.33 . 1 125 21 LYS HG3 H 1.33 . 1 126 21 LYS HD2 H 1.55 . 1 127 21 LYS HD3 H 1.55 . 1 128 21 LYS HE2 H 2.86 . 1 129 21 LYS HE3 H 2.86 . 1 130 22 LYS H H 8.39 . 1 131 22 LYS HA H 4.33 . 1 132 22 LYS HB2 H 1.77 . 2 133 22 LYS HB3 H 1.70 . 2 134 22 LYS HG2 H 1.41 . 2 135 22 LYS HG3 H 1.37 . 2 136 22 LYS HD2 H 1.64 . 1 137 22 LYS HD3 H 1.64 . 1 138 22 LYS HE2 H 2.93 . 1 139 22 LYS HE3 H 2.93 . 1 140 23 GLY H H 8.24 . 1 141 23 GLY HA2 H 3.75 . 2 142 23 GLY HA3 H 3.56 . 2 143 24 CYS H H 8.17 . 1 144 24 CYS HA H 4.00 . 1 145 24 CYS HB2 H 2.01 . 2 146 24 CYS HB3 H 2.86 . 2 147 25 TRP H H 8.60 . 1 148 25 TRP HA H 4.48 . 1 149 25 TRP HB2 H 3.40 . 2 150 25 TRP HB3 H 3.43 . 2 151 25 TRP HD1 H 7.34 . 1 152 25 TRP HE1 H 10.13 . 1 153 25 TRP HE3 H 7.60 . 1 154 25 TRP HZ2 H 7.50 . 1 155 25 TRP HZ3 H 7.14 . 1 156 25 TRP HH2 H 7.23 . 1 157 26 LYS H H 9.44 . 1 158 26 LYS HA H 4.25 . 1 159 26 LYS HB2 H 1.66 . 2 160 26 LYS HB3 H 2.24 . 2 161 26 LYS HG2 H 1.31 . 1 162 26 LYS HG3 H 1.31 . 1 163 26 LYS HD2 H 1.82 . 1 164 26 LYS HD3 H 1.82 . 1 165 26 LYS HE2 H 2.94 . 1 166 26 LYS HE3 H 2.94 . 1 167 27 CYS H H 8.69 . 1 168 27 CYS HA H 4.94 . 1 169 27 CYS HB2 H 2.53 . 2 170 27 CYS HB3 H 3.22 . 2 171 28 GLY H H 8.19 . 1 172 28 GLY HA2 H 3.85 . 2 173 28 GLY HA3 H 4.07 . 2 174 29 LYS H H 8.47 . 1 175 29 LYS HA H 4.37 . 1 176 29 LYS HB2 H 1.82 . 2 177 29 LYS HB3 H 1.88 . 2 178 29 LYS HG2 H 1.77 . 2 179 29 LYS HG3 H 1.60 . 2 180 29 LYS HD2 H 1.41 . 1 181 29 LYS HD3 H 1.41 . 1 182 29 LYS HE2 H 3.02 . 1 183 29 LYS HE3 H 3.02 . 1 184 30 GLU H H 8.55 . 1 185 30 GLU HA H 4.22 . 1 186 30 GLU HB2 H 1.86 . 2 187 30 GLU HB3 H 1.99 . 2 188 30 GLU HG2 H 2.11 . 2 189 30 GLU HG3 H 2.22 . 2 190 31 GLY H H 8.67 . 1 191 31 GLY HA2 H 4.34 . 2 192 31 GLY HA3 H 3.69 . 2 193 32 HIS H H 7.14 . 1 194 32 HIS HA H 4.78 . 1 195 32 HIS HB2 H 3.19 . 1 196 32 HIS HB3 H 3.19 . 1 197 32 HIS HD2 H 6.84 . 1 198 32 HIS HE1 H 7.48 . 1 199 33 GLN H H 8.95 . 1 200 33 GLN HA H 4.60 . 1 201 33 GLN HB2 H 1.92 . 1 202 33 GLN HB3 H 1.92 . 1 203 33 GLN HG2 H 2.37 . 2 204 33 GLN HG3 H 2.44 . 2 205 33 GLN HE21 H 6.88 . 2 206 33 GLN HE22 H 7.66 . 2 207 34 MET H H 8.94 . 1 208 34 MET HA H 4.83 . 1 209 34 MET HB2 H 2.15 . 1 210 34 MET HB3 H 2.15 . 1 211 34 MET HG2 H 2.51 . 1 212 34 MET HG3 H 2.51 . 1 213 34 MET HE H 2.09 . 1 214 35 LYS H H 8.63 . 1 215 35 LYS HA H 4.24 . 1 216 35 LYS HB2 H 1.73 . 2 217 35 LYS HB3 H 1.88 . 2 218 35 LYS HG2 H 1.22 . 1 219 35 LYS HG3 H 1.22 . 1 220 35 LYS HD2 H 1.33 . 1 221 35 LYS HD3 H 1.33 . 1 222 35 LYS HE2 H 3.00 . 1 223 35 LYS HE3 H 3.00 . 1 224 36 ASP H H 7.94 . 1 225 36 ASP HA H 4.89 . 1 226 36 ASP HB2 H 2.54 . 2 227 36 ASP HB3 H 2.96 . 2 228 37 CYS H H 7.69 . 1 229 37 CYS HA H 3.68 . 1 230 37 CYS HB2 H 2.87 . 2 231 37 CYS HB3 H 3.29 . 2 232 38 THR H H 8.32 . 1 233 38 THR HA H 4.45 . 1 234 38 THR HB H 4.42 . 1 235 38 THR HG2 H 1.08 . 1 236 39 GLU H H 8.62 . 1 237 39 GLU HA H 4.06 . 1 238 39 GLU HB2 H 1.86 . 2 239 39 GLU HB3 H 2.13 . 2 240 39 GLU HG2 H 2.21 . 2 241 39 GLU HG3 H 2.37 . 2 stop_ save_