data_6304 #Corrected using PDB structure: 1WYWB # #N.B. (Observed* = Observed shift + Offset correction) # #After reference correction, the following residues still #have a N chemical shift difference (obs*-pred) greater than 10.0ppm: #NUM AA CS Observed* Predicted # 75 A N 139.97 128.84 # #After reference correction, the following residues still #have a HN chemical shift difference (obs*-pred) greater than 2.0ppm: #NUM AA CS Observed* Predicted # 75 A H 11.00 8.84 # #The average CS difference between predicted and observed: #HA CA CB CO N HN #N/A N/A N/A N/A 0.46 0.06 # #bmr6304.str.corr chemical shifts have been re-referenced with the following #offsets (these values have been added to the original bmr6304.str file): #HA CA CB CO N HN #N/A N/A N/A N/A +0.46 N/A # #The 95% confidence intervals for the above recommended offsets are: # HA CA CB CO N HN # N/A N/A N/A N/A +/-0.45 +/-0.05 # #The Correlation Coefficients between predicted and observed #chemical shifts are: #HA CA CB CO N HN #N/A N/A N/A N/A 0.857 0.783 # #The RMSD between predicted and observed* (reference #corrected) chemical shifts are: #HA CA CB CO N HN #N/A N/A N/A N/A 1.947 0.239 # ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Amide chemical shifts of mature human SUMO-1 ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 McIntosh Lawrence P. . stop_ _BMRB_accession_number 6304 _BMRB_flat_file_name bmr6304.str _Entry_type new _Submission_date 2004-08-27 _Accession_date 2004-08-27 _Entry_origination author _NMR_STAR_version 2.1.1 _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' 93 '15N chemical shifts' 93 stop_ loop_ _Related_BMRB_accession_number _Relationship 6305 "RanGAP1 C-domain" 6306 "Sumoylated RanGAP1" stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title ; Structural and Dynamic Independence of Isopeptide-linked RanGAP1 and SUMO-1 ; _Citation_status published _Citation_type journal _MEDLINE_UI_code . _PubMed_ID 15355965 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Macauley Matthew S. . 2 Errington Wesley J. . 3 Okon Mark . . 4 Scharpf Manuela . . 5 Mackereth Cameron D. . 6 Schulman Brenda A. . 7 McIntosh Lawrence P. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 279 _Journal_issue 47 _Page_first 49131 _Page_last 49137 _Year 2004 loop_ _Keyword sumo "ubiquitin-like protein" stop_ save_ ################################## # Molecular system description # ################################## save_molecular_system _Saveframe_category molecular_system _Mol_system_name SUMO-1 _Abbreviation_common SUMO-1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label SUMO-1 $SUMO-1 stop_ _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state "all free" loop_ _Biological_function ; Sumoylation (covalent isopeptide linkage of Gly97 to the side chain amino group of a lysine in a target protein) ; stop_ _Details ; Residues 1-97 of mature human sumo-1 ; save_ ######################## # Monomeric polymers # ######################## save_SUMO-1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common SUMO-1 _Name_variant . _Abbreviation_common SUMO-1 _Mol_thiol_state "all free" ############################## # Polymer residue sequence # ############################## _Residue_count 100 _Mol_residue_sequence ; GSHMSDQEAKPSTEDLGDKK EGEYIKLKVIGQDSSEIHFK VKMTTHLKKLKESYCQRQGV PMNSLRFLFEGQRIADNHTP KELGMEEEDVIEVYQEQTGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -3 GLY 2 -2 SER 3 -1 HIS 4 1 MET 5 2 SER 6 3 ASP 7 4 GLN 8 5 GLU 9 6 ALA 10 7 LYS 11 8 PRO 12 9 SER 13 10 THR 14 11 GLU 15 12 ASP 16 13 LEU 17 14 GLY 18 15 ASP 19 16 LYS 20 17 LYS 21 18 GLU 22 19 GLY 23 20 GLU 24 21 TYR 25 22 ILE 26 23 LYS 27 24 LEU 28 25 LYS 29 26 VAL 30 27 ILE 31 28 GLY 32 29 GLN 33 30 ASP 34 31 SER 35 32 SER 36 33 GLU 37 34 ILE 38 35 HIS 39 36 PHE 40 37 LYS 41 38 VAL 42 39 LYS 43 40 MET 44 41 THR 45 42 THR 46 43 HIS 47 44 LEU 48 45 LYS 49 46 LYS 50 47 LEU 51 48 LYS 52 49 GLU 53 50 SER 54 51 TYR 55 52 CYS 56 53 GLN 57 54 ARG 58 55 GLN 59 56 GLY 60 57 VAL 61 58 PRO 62 59 MET 63 60 ASN 64 61 SER 65 62 LEU 66 63 ARG 67 64 PHE 68 65 LEU 69 66 PHE 70 67 GLU 71 68 GLY 72 69 GLN 73 70 ARG 74 71 ILE 75 72 ALA 76 73 ASP 77 74 ASN 78 75 HIS 79 76 THR 80 77 PRO 81 78 LYS 82 79 GLU 83 80 LEU 84 81 GLY 85 82 MET 86 83 GLU 87 84 GLU 88 85 GLU 89 86 ASP 90 87 VAL 91 88 ILE 92 89 GLU 93 90 VAL 94 91 TYR 95 92 GLN 96 93 GLU 97 94 GLN 98 95 THR 99 96 GLY 100 97 GLY stop_ _Sequence_homology_query_date 2005-09-22 _Sequence_homology_query_revised_last_date 2005-09-01 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 2BF8 "B Chain B, Crystal Structure Of Sumo ModifiedUbiquitin Conjugating Enzyme E2-25k" 129.87 77 100 100 2e-38 PDB 1TGZ "B Chain B, Structure Of Human Senp2 In ComplexWith Sumo-1" 125.00 80 100 100 3e-40 PDB 1Z5S "B Chain B, Crystal Structure Of A ComplexBetween Ubc9, Sumo-1, Rangap1 And Nup358RANBP2" 121.95 82 100 100 3e-40 PDB 1WYW "B Chain B, Crystal Structure OfSumo1-Conjugated Thymine Dna Glycosylase" 103.09 97 100 100 3e-50 PDB 1Y8R "C Chain C, Sumo E1 Activating EnzymeSae1-Sae2-Sumo1-Mg-Atp Complex" 103.09 97 100 100 3e-50 PDB 1A5R "Structure Determination Of The SmallUbiquitin-Related Modifier Sumo-1, Nmr, 10 Structures" 97.09 103 100 100 3e-50 DBJ BAB22172.1 "unnamed protein product [Mus musculus]" 99.01 101 100 100 3e-50 DBJ BAB27379.1 "unnamed protein product [Mus musculus]" 99.01 101 100 100 3e-50 DBJ BAB93477.1 "ubiquitin-homology domain protein PIC1[Homo sapiens]" 99.01 101 100 100 3e-50 DBJ BAC40739.1 "unnamed protein product [Mus musculus]" 99.01 101 100 100 3e-50 EMBL CAA67898.1 "SMT3C protein [Homo sapiens]" 99.01 101 100 100 3e-50 EMBL CAG46944.1 "UBL1 [Homo sapiens]" 99.01 101 100 100 3e-50 EMBL CAG46953.1 "UBL1 [Homo sapiens]" 99.01 101 100 100 3e-50 EMBL CAH92616.1 "hypothetical protein [Pongo pygmaeus]" 99.01 101 100 100 3e-50 EMBL CAG31129.1 "hypothetical protein [Gallus gallus]" 99.01 101 98 98 3e-49 GenBank AAH53528.1 "Small ubiquitin-like modifier 1, isoforma precursor [Homo sapiens]" 99.01 101 100 100 3e-50 GenBank AAH83158.1 "SMT3 suppressor of mif two 3 homolog 1[Mus musculus]" 99.01 101 100 100 3e-50 GenBank AAI02885.1 "Unknown (protein for MGC:128420) [Bostaurus]" 99.01 101 100 100 3e-50 GenBank AAP35278.1 "ubiquitin-like 1 (sentrin) [Homosapiens]" 99.01 101 100 100 3e-50 GenBank AAX32589.1 "SMT3 suppressor of mif two 3-like 1[synthetic construct]" 99.01 101 100 100 3e-50 REF NP_001005781.1 "small ubiquitin-like modifier 1isoform a precursor [Homo sapiens]" 99.01 101 100 100 3e-50 REF NP_001009672.1 "SMT3 suppressor of mif two 3homolog 1 [Rattus norvegicus]" 99.01 101 100 100 3e-50 REF NP_003343.1 "small ubiquitin-like modifier 1 isoforma precursor [Homo sapiens]" 99.01 101 100 100 3e-50 REF NP_033486.1 "SMT3 suppressor of mif two 3 homolog 1[Mus musculus]" 99.01 101 100 100 3e-50 REF XP_516035.1 "PREDICTED: similar to SMT3 suppressorof mif two 3 homolog 1; Ubiquitin-like 1; ubiquitin-like1, 12kD; ubiquitin-like 1 (sentrin); SMT3 specificprotease 2 [Pan troglodytes]" 99.01 101 100 100 3e-50 SWISS-PROT P63165 "SUMO1_HUMAN Small ubiquitin-related modifier1 precursor (SUMO-1) (Ubiquitin-like protein SMT3C)(SMT3 homolog 3) (Ubiquitin-homology domain proteinPIC1) (Ubiquitin-like protein UBL1) (GAP modifyingprotein 1) (GMP1) (Sentrin)" 99.01 101 100 100 3e-50 SWISS-PROT P63166 "SUMO1_MOUSE Small ubiquitin-related modifier1 precursor (SUMO-1) (Ubiquitin-like protein SMT3C)(SMT3 homolog 3) (Ubiquitin-homology domain proteinPIC1)" 99.01 101 100 100 3e-50 SWISS-PROT Q5E9D1 "SUMO1_BOVIN Small ubiquitin-related modifier1 precursor (SUMO-1)" 99.01 101 100 100 3e-50 SWISS-PROT Q5R6J4 "SUMO1_PONPY Small ubiquitin-related modifier1 precursor (SUMO-1)" 99.01 101 100 100 3e-50 SWISS-PROT Q9MZD5 "SUMO1_CERNI Small ubiquitin-related modifier1 precursor (SUMO-1) (Sentrin)" 99.01 101 99 99 1e-49 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Tissue $SUMO-1 "Homo sapian" 9606 Eukaryota Animalia Homo sapians . 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 $SUMO-1 'recombinant technology' 'E. coli' Escherichia coli BL21 pET28a stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SUMO-1 ? ? ? KCl 100 mM . KPhos 10 mM . DTT 2 mM . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_NMRpipe _Saveframe_category software _Name NMRpipe _Version ? save_ save_Felix _Saveframe_category software _Name Felix _Version ? save_ save_Sparky _Saveframe_category software _Name Sparky _Version ? save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity _Field_strength 500 save_ ############################# # NMR applied experiments # ############################# save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name ; 1H-15N HSQC 15N-editted NOESY-HSQC 15N-editted TOCSY-HSQC ; save_ ####################### # Sample conditions # ####################### save_sample_conditions _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 0.1 pH temperature 290 0 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference 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 DSS H 1 'methyl protons' ppm 0 direct external cylindrical "outside sample" parallel 1.0 DSS N 15 nitrogen ppm 0 indirect external cylindrical "outside sample" parallel 0.101329118 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # Index Value Definition # # # # 1 Unique (geminal atoms and geminal methyl # # groups with identical chemical shifts # # are assumed to be assigned to # # stereospecific atoms) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups # # 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) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts _Saveframe_category assigned_chemical_shifts loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name SUMO-1 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 5 SER H H 8.46 0.02 1 2 5 SER N N 117.50 0.1 1 3 6 ASP H H 8.47 0.02 1 4 6 ASP N N 122.79 0.1 1 5 7 GLN H H 8.26 0.02 1 7 8 GLU H H 8.28 0.02 1 8 8 GLU N N 122.04 0.1 1 9 9 ALA H H 8.28 0.02 1 10 9 ALA N N 125.87 0.1 1 11 10 LYS H H 8.32 0.02 1 12 10 LYS N N 122.82 0.1 1 13 12 SER H H 8.61 0.02 1 14 12 SER N N 117.41 0.1 1 15 13 THR H H 8.26 0.02 1 16 13 THR N N 116.37 0.1 1 17 14 GLU H H 8.38 0.02 1 18 14 GLU N N 123.57 0.1 1 19 15 ASP H H 8.43 0.02 1 20 15 ASP N N 122.72 0.1 1 21 16 LEU H H 8.41 0.02 1 22 16 LEU N N 124.24 0.1 1 23 17 GLY H H 8.47 0.02 1 24 17 GLY N N 109.44 0.1 1 25 18 ASP H H 8.22 0.02 1 26 18 ASP N N 120.95 0.1 1 27 19 LYS H H 8.45 0.02 1 28 19 LYS N N 122.59 0.1 1 29 20 LYS H H 8.36 0.02 1 30 20 LYS N N 122.61 0.1 1 31 21 GLU H H 8.51 0.02 1 32 21 GLU N N 122.41 0.1 1 33 22 GLY H H 8.47 0.02 1 34 22 GLY N N 110.20 0.1 1 35 23 GLU H H 8.32 0.02 1 36 23 GLU N N 121.82 0.1 1 37 24 TYR H H 8.38 0.02 1 38 24 TYR N N 119.85 0.1 1 39 25 ILE H H 9.18 0.02 1 40 25 ILE N N 117.22 0.1 1 41 26 LYS H H 8.63 0.02 1 42 26 LYS N N 124.86 0.1 1 43 27 LEU H H 8.95 0.02 1 44 27 LEU N N 124.65 0.1 1 45 28 LYS H H 8.64 0.02 1 46 28 LYS N N 121.19 0.1 1 47 29 VAL H H 9.12 0.02 1 48 29 VAL N N 124.62 0.1 1 49 30 ILE H H 9.09 0.02 1 50 30 ILE N N 128.81 0.1 1 51 31 GLY H H 8.49 0.02 1 52 31 GLY N N 113.83 0.1 1 53 32 GLN H H 8.77 0.02 1 54 32 GLN N N 121.01 0.1 1 55 33 ASP H H 8.35 0.02 1 56 33 ASP N N 118.87 0.1 1 57 34 SER H H 8.02 0.02 1 58 34 SER N N 111.63 0.1 1 59 35 SER H H 8.10 0.02 1 60 35 SER N N 118.01 0.1 1 61 36 GLU H H 8.63 0.02 1 62 36 GLU N N 122.27 0.1 1 63 37 ILE H H 8.83 0.02 1 64 37 ILE N N 125.55 0.1 1 65 38 HIS H H 8.70 0.02 1 66 38 HIS N N 126.16 0.1 1 67 39 PHE H H 9.12 0.02 1 68 39 PHE N N 120.50 0.1 1 69 40 LYS H H 8.79 0.02 1 70 40 LYS N N 124.28 0.1 1 71 41 VAL H H 9.16 0.02 1 72 41 VAL N N 120.19 0.1 1 73 42 LYS H H 8.63 0.02 1 74 42 LYS N N 122.83 0.1 1 75 43 MET H H 8.59 0.02 1 76 43 MET N N 120.49 0.1 1 77 44 THR H H 7.00 0.02 1 78 44 THR N N 100.64 0.1 1 79 45 THR H H 7.20 0.02 1 80 45 THR N N 121.11 0.1 1 81 46 HIS H H 8.82 0.02 1 82 46 HIS N N 126.83 0.1 1 83 47 LEU H H 9.37 0.02 1 84 47 LEU N N 125.29 0.1 1 85 48 LYS H H 8.55 0.02 1 86 48 LYS N N 121.92 0.1 1 87 49 LYS H H 7.52 0.02 1 88 49 LYS N N 114.54 0.1 1 89 50 LEU H H 6.75 0.02 1 90 50 LEU N N 122.43 0.1 1 91 51 LYS H H 7.58 0.02 1 92 51 LYS N N 118.76 0.1 1 93 52 GLU H H 8.52 0.02 1 94 52 GLU N N 118.62 0.1 1 95 53 SER H H 7.98 0.02 1 96 53 SER N N 116.19 0.1 1 97 54 TYR H H 8.86 0.02 1 98 54 TYR N N 123.19 0.1 1 99 55 CYS H H 8.69 0.02 1 100 55 CYS N N 117.93 0.1 1 101 56 GLN H H 8.34 0.02 1 102 56 GLN N N 119.71 0.1 1 103 57 ARG H H 8.03 0.02 1 105 58 GLN H H 7.82 0.02 1 106 58 GLN N N 114.67 0.1 1 107 59 GLY H H 7.95 0.02 1 108 59 GLY N N 110.28 0.1 1 109 60 VAL H H 7.67 0.02 1 110 60 VAL N N 112.53 0.1 1 111 62 MET H H 9.02 0.02 1 112 62 MET N N 125.03 0.1 1 113 63 ASN H H 8.44 0.02 1 114 63 ASN N N 113.71 0.1 1 115 64 SER H H 7.95 0.02 1 116 64 SER N N 113.61 0.1 1 117 65 LEU H H 7.28 0.02 1 118 65 LEU N N 121.47 0.1 1 119 66 ARG H H 9.01 0.02 1 120 66 ARG N N 120.67 0.1 1 121 67 PHE H H 8.94 0.02 1 122 67 PHE N N 123.05 0.1 1 123 68 LEU H H 9.76 0.02 1 124 68 LEU N N 124.73 0.1 1 125 69 PHE H H 8.98 0.02 1 126 69 PHE N N 119.91 0.1 1 127 70 GLU H H 9.39 0.02 1 128 70 GLU N N 129.75 0.1 1 129 71 GLY H H 8.88 0.02 1 130 71 GLY N N 103.66 0.1 1 131 72 GLN H H 8.01 0.02 1 132 72 GLN N N 121.22 0.1 1 133 73 ARG H H 8.69 0.02 1 134 73 ARG N N 124.95 0.1 1 135 74 ILE H H 9.04 0.02 1 136 74 ILE N N 127.46 0.1 1 137 75 ALA H H 10.94 0.02 1 138 75 ALA N N 139.97 0.1 1 139 76 ASP H H 8.78 0.02 1 141 77 ASN H H 7.75 0.02 1 142 77 ASN N N 110.04 0.1 1 143 78 HIS H H 7.17 0.02 1 144 78 HIS N N 120.33 0.1 1 145 79 THR H H 7.33 0.02 1 146 79 THR N N 108.83 0.1 1 147 81 LYS H H 8.10 0.02 1 148 81 LYS N N 115.85 0.1 1 149 82 GLU H H 7.99 0.02 1 150 82 GLU N N 121.30 0.1 1 151 83 LEU H H 7.50 0.02 1 152 83 LEU N N 115.63 0.1 1 153 84 GLY H H 7.66 0.02 1 154 84 GLY N N 108.56 0.1 1 155 85 MET H H 7.64 0.02 1 156 85 MET N N 118.22 0.1 1 157 86 GLU H H 9.33 0.02 1 158 86 GLU N N 121.58 0.1 1 159 87 GLU H H 8.30 0.02 1 160 87 GLU N N 120.39 0.1 1 161 88 GLU H H 9.38 0.02 1 162 88 GLU N N 119.47 0.1 1 163 89 ASP H H 8.17 0.02 1 164 89 ASP N N 120.80 0.1 1 165 90 VAL H H 8.21 0.02 1 166 90 VAL N N 117.19 0.1 1 167 91 ILE H H 9.17 0.02 1 168 91 ILE N N 127.85 0.1 1 169 92 GLU H H 8.87 0.02 1 170 92 GLU N N 126.36 0.1 1 171 93 VAL H H 7.79 0.02 1 172 93 VAL N N 120.26 0.1 1 173 94 TYR H H 8.55 0.02 1 174 94 TYR N N 124.74 0.1 1 175 95 GLN H H 8.74 0.02 1 176 95 GLN N N 121.30 0.1 1 177 96 GLU H H 8.44 0.02 1 178 96 GLU N N 125.66 0.1 1 179 97 GLN H H 8.80 0.02 1 181 98 THR H H 8.41 0.02 1 183 99 GLY H H 8.52 0.02 1 185 100 GLY H H 8.04 0.02 1 stop_ save_