0.020777 0.000000 0.000000 0.000000 0.019600 0.000000 0.000000 0.000000 0.024673 0.00000 0.00000 0.00000 Zegers, I. Wyns, L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 48.130 51.020 40.530 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking Ca 2 40.078 CALCIUM ION non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C10 H12 N5 O6 P S 361.271 GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE non-polymer C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Nat.Struct.Biol. NSBIEW 2024 1072-8368 5 280 283 10.1038/nsb0498-280 9546218 Hydrolysis of a slow cyclic thiophosphate substrate of RNase T1 analyzed by time-resolved crystallography. 1998 10.2210/pdb1gsp/pdb pdb_00001gsp 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 293 1 IMAGE PLATE 1997-07 MARRESEARCH GRAPHITE(002) M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU COMPLEX WITH GUANOSINE 2',3' CYCLIC PHOSPHOROTHIOATE 11094.694 RIBONUCLEASE T1 3.1.27.3 1 man polymer 40.078 CALCIUM ION 1 syn non-polymer 361.271 GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE 1 syn non-polymer 18.015 water 123 nat water RNASE T1 no no ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVF NENNQLAGVITHTGASGNNFVECT ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVF NENNQLAGVITHTGASGNNFVECT A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Aspergillus Escherichia sample 5062 Aspergillus oryzae 562 Escherichia coli 1 3.86 35.2 4.2 20 MM NAAC PH 4.2 2 MM CACL2 55 % MPD database_2 pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Refinement description 1 0 1998-02-25 1 1 2008-03-24 1 2 2011-07-13 1 3 2023-08-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1997-11-28 REL REL CA CALCIUM ION SGP GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE HOH water 1RGA PDB ENTRY 1RGA PDB experimental model CA 106 2 CA CA 106 A SGP 105 3 SGP SGP 105 A HOH 107 4 HOH HOH 107 A HOH 108 4 HOH HOH 108 A HOH 109 4 HOH HOH 109 A HOH 110 4 HOH HOH 110 A HOH 111 4 HOH HOH 111 A HOH 112 4 HOH HOH 112 A HOH 113 4 HOH HOH 113 A HOH 114 4 HOH HOH 114 A HOH 115 4 HOH HOH 115 A HOH 116 4 HOH HOH 116 A HOH 117 4 HOH HOH 117 A HOH 118 4 HOH HOH 118 A HOH 119 4 HOH HOH 119 A HOH 120 4 HOH HOH 120 A HOH 121 4 HOH HOH 121 A HOH 122 4 HOH HOH 122 A HOH 123 4 HOH HOH 123 A HOH 124 4 HOH HOH 124 A HOH 125 4 HOH HOH 125 A HOH 126 4 HOH HOH 126 A HOH 127 4 HOH HOH 127 A HOH 128 4 HOH HOH 128 A HOH 129 4 HOH HOH 129 A HOH 130 4 HOH HOH 130 A HOH 131 4 HOH HOH 131 A HOH 132 4 HOH HOH 132 A HOH 133 4 HOH HOH 133 A HOH 134 4 HOH HOH 134 A HOH 135 4 HOH HOH 135 A HOH 136 4 HOH HOH 136 A HOH 137 4 HOH HOH 137 A HOH 138 4 HOH HOH 138 A HOH 139 4 HOH HOH 139 A HOH 140 4 HOH HOH 140 A HOH 141 4 HOH HOH 141 A HOH 142 4 HOH HOH 142 A HOH 143 4 HOH HOH 143 A HOH 144 4 HOH HOH 144 A HOH 145 4 HOH HOH 145 A HOH 146 4 HOH HOH 146 A HOH 147 4 HOH HOH 147 A HOH 148 4 HOH HOH 148 A HOH 149 4 HOH HOH 149 A HOH 150 4 HOH HOH 150 A HOH 151 4 HOH HOH 151 A HOH 152 4 HOH HOH 152 A HOH 153 4 HOH HOH 153 A HOH 154 4 HOH HOH 154 A HOH 155 4 HOH HOH 155 A HOH 156 4 HOH HOH 156 A HOH 157 4 HOH HOH 157 A HOH 158 4 HOH HOH 158 A HOH 159 4 HOH HOH 159 A HOH 160 4 HOH HOH 160 A HOH 161 4 HOH HOH 161 A HOH 162 4 HOH HOH 162 A HOH 163 4 HOH HOH 163 A HOH 164 4 HOH HOH 164 A HOH 165 4 HOH HOH 165 A HOH 166 4 HOH HOH 166 A HOH 167 4 HOH HOH 167 A HOH 168 4 HOH HOH 168 A HOH 169 4 HOH HOH 169 A HOH 170 4 HOH HOH 170 A HOH 171 4 HOH HOH 171 A HOH 172 4 HOH HOH 172 A HOH 173 4 HOH HOH 173 A HOH 174 4 HOH HOH 174 A HOH 175 4 HOH HOH 175 A HOH 176 4 HOH HOH 176 A HOH 177 4 HOH HOH 177 A HOH 178 4 HOH HOH 178 A HOH 179 4 HOH HOH 179 A HOH 180 4 HOH HOH 180 A HOH 181 4 HOH HOH 181 A HOH 182 4 HOH HOH 182 A HOH 183 4 HOH HOH 183 A HOH 184 4 HOH HOH 184 A HOH 185 4 HOH HOH 185 A HOH 186 4 HOH HOH 186 A HOH 187 4 HOH HOH 187 A HOH 188 4 HOH HOH 188 A HOH 189 4 HOH HOH 189 A HOH 190 4 HOH HOH 190 A HOH 191 4 HOH HOH 191 A HOH 192 4 HOH HOH 192 A HOH 193 4 HOH HOH 193 A HOH 194 4 HOH HOH 194 A HOH 195 4 HOH HOH 195 A HOH 196 4 HOH HOH 196 A HOH 197 4 HOH HOH 197 A HOH 198 4 HOH HOH 198 A HOH 199 4 HOH HOH 199 A HOH 200 4 HOH HOH 200 A HOH 201 4 HOH HOH 201 A HOH 202 4 HOH HOH 202 A HOH 203 4 HOH HOH 203 A HOH 204 4 HOH HOH 204 A HOH 205 4 HOH HOH 205 A HOH 206 4 HOH HOH 206 A HOH 207 4 HOH HOH 207 A HOH 208 4 HOH HOH 208 A HOH 209 4 HOH HOH 209 A HOH 210 4 HOH HOH 210 A HOH 211 4 HOH HOH 211 A HOH 212 4 HOH HOH 212 A HOH 213 4 HOH HOH 213 A HOH 214 4 HOH HOH 214 A HOH 215 4 HOH HOH 215 A HOH 216 4 HOH HOH 216 A HOH 217 4 HOH HOH 217 A HOH 218 4 HOH HOH 218 A HOH 219 4 HOH HOH 219 A HOH 220 4 HOH HOH 220 A HOH 221 4 HOH HOH 221 A HOH 222 4 HOH HOH 222 A HOH 223 4 HOH HOH 223 A HOH 224 4 HOH HOH 224 A HOH 225 4 HOH HOH 225 A HOH 226 4 HOH HOH 226 A HOH 227 4 HOH HOH 227 A HOH 228 4 HOH HOH 228 A HOH 229 4 HOH HOH 229 A ALA 1 n 1 ALA 1 A CYS 2 n 2 CYS 2 A ASP 3 n 3 ASP 3 A TYR 4 n 4 TYR 4 A THR 5 n 5 THR 5 A CYS 6 n 6 CYS 6 A GLY 7 n 7 GLY 7 A SER 8 n 8 SER 8 A ASN 9 n 9 ASN 9 A CYS 10 n 10 CYS 10 A TYR 11 n 11 TYR 11 A SER 12 n 12 SER 12 A SER 13 n 13 SER 13 A SER 14 n 14 SER 14 A ASP 15 n 15 ASP 15 A VAL 16 n 16 VAL 16 A SER 17 n 17 SER 17 A THR 18 n 18 THR 18 A ALA 19 n 19 ALA 19 A GLN 20 n 20 GLN 20 A ALA 21 n 21 ALA 21 A ALA 22 n 22 ALA 22 A GLY 23 n 23 GLY 23 A TYR 24 n 24 TYR 24 A LYS 25 n 25 LYS 25 A LEU 26 n 26 LEU 26 A HIS 27 n 27 HIS 27 A GLU 28 n 28 GLU 28 A ASP 29 n 29 ASP 29 A GLY 30 n 30 GLY 30 A GLU 31 n 31 GLU 31 A THR 32 n 32 THR 32 A VAL 33 n 33 VAL 33 A GLY 34 n 34 GLY 34 A SER 35 n 35 SER 35 A ASN 36 n 36 ASN 36 A SER 37 n 37 SER 37 A TYR 38 n 38 TYR 38 A PRO 39 n 39 PRO 39 A HIS 40 n 40 HIS 40 A LYS 41 n 41 LYS 41 A TYR 42 n 42 TYR 42 A ASN 43 n 43 ASN 43 A ASN 44 n 44 ASN 44 A TYR 45 n 45 TYR 45 A GLU 46 n 46 GLU 46 A GLY 47 n 47 GLY 47 A PHE 48 n 48 PHE 48 A ASP 49 n 49 ASP 49 A PHE 50 n 50 PHE 50 A SER 51 n 51 SER 51 A VAL 52 n 52 VAL 52 A SER 53 n 53 SER 53 A SER 54 n 54 SER 54 A PRO 55 n 55 PRO 55 A TYR 56 n 56 TYR 56 A TYR 57 n 57 TYR 57 A GLU 58 n 58 GLU 58 A TRP 59 n 59 TRP 59 A PRO 60 n 60 PRO 60 A ILE 61 n 61 ILE 61 A LEU 62 n 62 LEU 62 A SER 63 n 63 SER 63 A SER 64 n 64 SER 64 A GLY 65 n 65 GLY 65 A ASP 66 n 66 ASP 66 A VAL 67 n 67 VAL 67 A TYR 68 n 68 TYR 68 A SER 69 n 69 SER 69 A GLY 70 n 70 GLY 70 A GLY 71 n 71 GLY 71 A SER 72 n 72 SER 72 A PRO 73 n 73 PRO 73 A GLY 74 n 74 GLY 74 A ALA 75 n 75 ALA 75 A ASP 76 n 76 ASP 76 A ARG 77 n 77 ARG 77 A VAL 78 n 78 VAL 78 A VAL 79 n 79 VAL 79 A PHE 80 n 80 PHE 80 A ASN 81 n 81 ASN 81 A GLU 82 n 82 GLU 82 A ASN 83 n 83 ASN 83 A ASN 84 n 84 ASN 84 A GLN 85 n 85 GLN 85 A LEU 86 n 86 LEU 86 A ALA 87 n 87 ALA 87 A GLY 88 n 88 GLY 88 A VAL 89 n 89 VAL 89 A ILE 90 n 90 ILE 90 A THR 91 n 91 THR 91 A HIS 92 n 92 HIS 92 A THR 93 n 93 THR 93 A GLY 94 n 94 GLY 94 A ALA 95 n 95 ALA 95 A SER 96 n 96 SER 96 A GLY 97 n 97 GLY 97 A ASN 98 n 98 ASN 98 A ASN 99 n 99 ASN 99 A PHE 100 n 100 PHE 100 A VAL 101 n 101 VAL 101 A GLU 102 n 102 GLU 102 A CYS 103 n 103 CYS 103 A THR 104 n 104 THR 104 A author_defined_assembly 1 monomeric A ASP 15 A OD1 ASP 15 1_555 A CA 106 B CA CA 1_555 A ASP 15 A OD2 ASP 15 1_555 52.9 A ASP 15 A OD1 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 116 D O HOH 1_555 127.3 A ASP 15 A OD2 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 116 D O HOH 1_555 74.3 A ASP 15 A OD1 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 136 D O HOH 1_555 83.2 A ASP 15 A OD2 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 136 D O HOH 1_555 136.2 A HOH 116 D O HOH 1_555 A CA 106 B CA CA 1_555 A HOH 136 D O HOH 1_555 149.3 A ASP 15 A OD1 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 145 D O HOH 1_555 74.3 A ASP 15 A OD2 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 145 D O HOH 1_555 77.5 A HOH 116 D O HOH 1_555 A CA 106 B CA CA 1_555 A HOH 145 D O HOH 1_555 97.3 A HOH 136 D O HOH 1_555 A CA 106 B CA CA 1_555 A HOH 145 D O HOH 1_555 93.9 A ASP 15 A OD1 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 153 D O HOH 2_574 147.4 A ASP 15 A OD2 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 153 D O HOH 2_574 140.8 A HOH 116 D O HOH 1_555 A CA 106 B CA CA 1_555 A HOH 153 D O HOH 2_574 76.3 A HOH 136 D O HOH 1_555 A CA 106 B CA CA 1_555 A HOH 153 D O HOH 2_574 77.4 A HOH 145 D O HOH 1_555 A CA 106 B CA CA 1_555 A HOH 153 D O HOH 2_574 81.1 A ASP 15 A OD1 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 160 D O HOH 1_555 78.2 A ASP 15 A OD2 ASP 15 1_555 A CA 106 B CA CA 1_555 A HOH 160 D O HOH 1_555 76.5 A HOH 116 D O HOH 1_555 A CA 106 B CA CA 1_555 A HOH 160 D O HOH 1_555 89.8 A HOH 136 D O HOH 1_555 A CA 106 B CA CA 1_555 A HOH 160 D O HOH 1_555 94.6 A HOH 145 D O HOH 1_555 A CA 106 B CA CA 1_555 A HOH 160 D O HOH 1_555 150.0 A HOH 153 D O HOH 2_574 A CA 106 B CA CA 1_555 A HOH 160 D O HOH 1_555 128.8 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N TYR 4 A N TYR 4 A O TYR 11 A O TYR 11 A N HIS 40 A N HIS 40 A O GLU 58 A O GLU 58 A N TRP 59 A N TRP 59 A O VAL 78 A O VAL 78 A N ARG 77 A N ARG 77 A O ILE 90 A O ILE 90 A O THR 91 A O THR 91 A N VAL 101 A N VAL 101 1 A SER 37 47.97 75.50 1 A ASN 81 -110.31 -168.52 PARAM19X.PRO TOPH19X.PRO PARHCSDX.PRO TOPHCSDX.PRO 21.1 0.206 0.02 0.151 0.151 2.20 15.0 548 5036 10.0 93.6 RANDOM 1000000. 0.001 1 THROUGHOUT 0.0 MOLECULAR REPLACEMENT PDB ENTRY 1RGA 2.20 15.0 123 928 1 23 781 0.06 1.715 25.50 1.474 0.225 0.02 0.21 2.3 75 539 8 12.2 93.0 18.63 2.2 20.0 1GSP 5152 0. 0.115 1 13.95 10.7 93.9 2.20 2.28 6.1 0.33 5. 88.3 data reduction DENZO data scaling SCALEPACK model building X-PLOR 3.851 refinement X-PLOR 3.851 phasing X-PLOR 3.851 RIBONUCLEASE T1 COMPLEXED WITH 2',3'-CGPS, 1 DAY 1 N N 2 N N 3 N N 4 N N A SER 13 A SER 13 HELX_P A ASP 29 A ASP 29 1 A 17 disulf 2.025 A CYS 2 A SG CYS 2 1_555 A CYS 10 A SG CYS 10 1_555 disulf 2.030 A CYS 6 A SG CYS 6 1_555 A CYS 103 A SG CYS 103 1_555 metalc 2.510 A ASP 15 A OD1 ASP 15 1_555 A CA 106 B CA CA 1_555 metalc 2.429 A ASP 15 A OD2 ASP 15 1_555 A CA 106 B CA CA 1_555 metalc 2.670 A CA 106 B CA CA 1_555 A HOH 116 D O HOH 1_555 metalc 2.388 A CA 106 B CA CA 1_555 A HOH 136 D O HOH 1_555 metalc 2.647 A CA 106 B CA CA 1_555 A HOH 145 D O HOH 1_555 metalc 2.815 A CA 106 B CA CA 1_555 A HOH 153 D O HOH 2_574 metalc 2.828 A CA 106 B CA CA 1_555 A HOH 160 D O HOH 1_555 ENDORIBONUCLEASE HYDROLASE, ENDORIBONUCLEASE A TYR 38 A TYR 38 1 A PRO 39 A PRO 39 0.00 A SER 54 A SER 54 1 A PRO 55 A PRO 55 -0.05 RNT1_ASPOR UNP 1 1 P00651 MKKTAIAIAVALAGFATVAQAACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEW PILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT 22 125 1GSP 1 104 P00651 A 1 1 104 2 5 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A TYR 4 A TYR 4 A CYS 6 A CYS 6 A ASN 9 A ASN 9 A SER 12 A SER 12 A PRO 39 A PRO 39 A TYR 42 A TYR 42 A PRO 55 A PRO 55 A LEU 62 A LEU 62 A ASP 76 A ASP 76 A ASN 81 A ASN 81 A GLN 85 A GLN 85 A THR 91 A THR 91 A PHE 100 A PHE 100 A CYS 103 A CYS 103 ACTIVE SITE. Unknown 5 SITE. Unknown 5 SITE. Unknown 1 BINDING SITE FOR RESIDUE CA A 106 A CA 106 Software 6 BINDING SITE FOR RESIDUE SGP A 105 A SGP 105 Software 16 A TYR 38 A TYR 38 5 1_555 A HIS 40 A HIS 40 5 1_555 A GLU 58 A GLU 58 5 1_555 A ARG 77 A ARG 77 5 1_555 A HIS 92 A HIS 92 5 1_555 A TYR 42 A TYR 42 5 1_555 A ASN 43 A ASN 43 5 1_555 A ASN 44 A ASN 44 5 1_555 A TYR 45 A TYR 45 5 1_555 A GLU 46 A GLU 46 5 1_555 A ASP 15 A ASP 15 1 1_555 A ASP 15 A ASP 15 6 1_555 A HOH 116 D HOH 6 1_555 A HOH 136 D HOH 6 1_555 A HOH 145 D HOH 6 1_555 A HOH 153 D HOH 6 2_574 A HOH 160 D HOH 6 1_555 A TYR 38 A TYR 38 16 1_555 A HIS 40 A HIS 40 16 1_555 A LYS 41 A LYS 41 16 1_555 A TYR 42 A TYR 42 16 1_555 A ASN 43 A ASN 43 16 1_555 A ASN 44 A ASN 44 16 1_555 A TYR 45 A TYR 45 16 1_555 A GLU 46 A GLU 46 16 1_555 A GLU 58 A GLU 58 16 1_555 A ARG 77 A ARG 77 16 1_555 A HIS 92 A HIS 92 16 1_555 A ASN 98 A ASN 98 16 1_555 A PHE 100 A PHE 100 16 1_555 A HOH 117 D HOH 16 1_555 A HOH 148 D HOH 16 1_555 A HOH 205 D HOH 16 1_555 19 P 21 21 21