0.021097 0.000000 0.000000 0.000000 0.021097 0.000000 0.000000 0.000000 0.015924 0.00000 0.00000 0.00000 Wynn, R. Harkins, P.C. Richards, F.M. Fox, R.O. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 47.400 47.400 62.800 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 C5 H11 N O2 S 149.211 y METHIONINE 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 H16 N2 O11 P2 402.188 THYMIDINE-3',5'-DIPHOSPHATE DNA linking 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 Protein Sci. PRCIEI 0795 0961-8368 5 1026 1031 8762134 Mobile unnatural amino acid side chains in the core of staphylococcal nuclease. 1996 US Protein Sci. PRCIEI 0795 0961-8368 4 1815 Interactions in Nonnative and Truncated Forms of Staphylococcal Nuclease as Indicated by Mutational Free Energy Changes 1995 10.2210/pdb1nuc/pdb pdb_00001nuc 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 278.15 1 COLLIMATOR IMAGE PLATE 1996-01 MACSCIENCE NI FILTER M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RUH2R PDTP, 3',5'-THYMIDINE DIPHOSPHATE 16847.342 STAPHYLOCOCCAL NUCLEASE 3.1.31.1 V23C 1 man polymer 40.078 CALCIUM ION 1 syn non-polymer 402.188 THYMIDINE-3',5'-DIPHOSPHATE 1 syn non-polymer 18.015 water 39 nat water no no ATSTKKLHKEPATLIKAIDGDTCKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ ATSTKKLHKEPATLIKAIDGDTCKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ 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 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 Staphylococcus Escherichia sample 1280 Staphylococcus aureus 562 Escherichia coli AR120 PAS1 1 2.09 41.23 8.15 10 MM POTASSIUM PHOSPHATE, PH = 8.15, PROTEIN CONC. = 2 MGS/ML, MPD = 21%, T = 4 C, temperature 277K 277 database_2 pdbx_database_status pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Refinement description 1 0 1997-06-16 1 1 2008-03-24 1 2 2011-07-13 1 3 2021-11-03 1 4 2023-08-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _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.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.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_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1997-02-15 REL CA CALCIUM ION THP THYMIDINE-3',5'-DIPHOSPHATE HOH water 1SNC PDB ENTRY 1SNC PDB experimental model CA 142 2 CA CA 150 A THP 143 3 THP THP 151 A HOH 201 4 HOH HOH 201 A HOH 202 4 HOH HOH 202 A HOH 204 4 HOH HOH 204 A HOH 206 4 HOH HOH 206 A HOH 208 4 HOH HOH 208 A HOH 209 4 HOH HOH 209 A HOH 211 4 HOH HOH 211 A HOH 213 4 HOH HOH 213 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 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 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 HOH 230 4 HOH HOH 230 A HOH 231 4 HOH HOH 231 A HOH 232 4 HOH HOH 232 A HOH 233 4 HOH HOH 233 A HOH 236 4 HOH HOH 236 A HOH 237 4 HOH HOH 237 A HOH 240 4 HOH HOH 240 A HOH 241 4 HOH HOH 241 A HOH 242 4 HOH HOH 242 A HOH 243 4 HOH HOH 243 A HOH 244 4 HOH HOH 244 A HOH 245 4 HOH HOH 245 A HOH 246 4 HOH HOH 246 A HOH 248 4 HOH HOH 248 A HOH 250 4 HOH HOH 250 A HOH 251 4 HOH HOH 251 A HOH 254 4 HOH HOH 254 A HOH 256 4 HOH HOH 256 A HOH 257 4 HOH HOH 257 A n 1 1 A n 2 2 A n 3 3 A n 4 4 A n 5 5 A n 6 6 A LEU 7 n 7 LEU 7 A HIS 8 n 8 HIS 8 A LYS 9 n 9 LYS 9 A GLU 10 n 10 GLU 10 A PRO 11 n 11 PRO 11 A ALA 12 n 12 ALA 12 A THR 13 n 13 THR 13 A LEU 14 n 14 LEU 14 A ILE 15 n 15 ILE 15 A LYS 16 n 16 LYS 16 A ALA 17 n 17 ALA 17 A ILE 18 n 18 ILE 18 A ASP 19 n 19 ASP 19 A GLY 20 n 20 GLY 20 A ASP 21 n 21 ASP 21 A THR 22 n 22 THR 22 A CYS 23 n 23 CYS 23 A LYS 24 n 24 LYS 24 A LEU 25 n 25 LEU 25 A MET 26 n 26 MET 26 A TYR 27 n 27 TYR 27 A LYS 28 n 28 LYS 28 A GLY 29 n 29 GLY 29 A GLN 30 n 30 GLN 30 A PRO 31 n 31 PRO 31 A MET 32 n 32 MET 32 A THR 33 n 33 THR 33 A PHE 34 n 34 PHE 34 A ARG 35 n 35 ARG 35 A LEU 36 n 36 LEU 36 A LEU 37 n 37 LEU 37 A LEU 38 n 38 LEU 38 A VAL 39 n 39 VAL 39 A ASP 40 n 40 ASP 40 A THR 41 n 41 THR 41 A PRO 42 n 42 PRO 42 A GLU 43 n 43 GLU 43 A THR 44 n 44 THR 44 A LYS 45 n 45 LYS 45 A HIS 46 n 46 HIS 46 A PRO 47 n 47 PRO 47 A LYS 48 n 48 LYS 48 A LYS 49 n 49 LYS 49 A GLY 50 n 50 GLY 50 A VAL 51 n 51 VAL 51 A GLU 52 n 52 GLU 52 A LYS 53 n 53 LYS 53 A TYR 54 n 54 TYR 54 A GLY 55 n 55 GLY 55 A PRO 56 n 56 PRO 56 A GLU 57 n 57 GLU 57 A ALA 58 n 58 ALA 58 A SER 59 n 59 SER 59 A ALA 60 n 60 ALA 60 A PHE 61 n 61 PHE 61 A THR 62 n 62 THR 62 A LYS 63 n 63 LYS 63 A LYS 64 n 64 LYS 64 A MET 65 n 65 MET 65 A VAL 66 n 66 VAL 66 A GLU 67 n 67 GLU 67 A ASN 68 n 68 ASN 68 A ALA 69 n 69 ALA 69 A LYS 70 n 70 LYS 70 A LYS 71 n 71 LYS 71 A ILE 72 n 72 ILE 72 A GLU 73 n 73 GLU 73 A VAL 74 n 74 VAL 74 A GLU 75 n 75 GLU 75 A PHE 76 n 76 PHE 76 A ASP 77 n 77 ASP 77 A LYS 78 n 78 LYS 78 A GLY 79 n 79 GLY 79 A GLN 80 n 80 GLN 80 A ARG 81 n 81 ARG 81 A THR 82 n 82 THR 82 A ASP 83 n 83 ASP 83 A LYS 84 n 84 LYS 84 A TYR 85 n 85 TYR 85 A GLY 86 n 86 GLY 86 A ARG 87 n 87 ARG 87 A GLY 88 n 88 GLY 88 A LEU 89 n 89 LEU 89 A ALA 90 n 90 ALA 90 A TYR 91 n 91 TYR 91 A ILE 92 n 92 ILE 92 A TYR 93 n 93 TYR 93 A ALA 94 n 94 ALA 94 A ASP 95 n 95 ASP 95 A GLY 96 n 96 GLY 96 A LYS 97 n 97 LYS 97 A MET 98 n 98 MET 98 A VAL 99 n 99 VAL 99 A ASN 100 n 100 ASN 100 A GLU 101 n 101 GLU 101 A ALA 102 n 102 ALA 102 A LEU 103 n 103 LEU 103 A VAL 104 n 104 VAL 104 A ARG 105 n 105 ARG 105 A GLN 106 n 106 GLN 106 A GLY 107 n 107 GLY 107 A LEU 108 n 108 LEU 108 A ALA 109 n 109 ALA 109 A LYS 110 n 110 LYS 110 A VAL 111 n 111 VAL 111 A ALA 112 n 112 ALA 112 A TYR 113 n 113 TYR 113 A VAL 114 n 114 VAL 114 A TYR 115 n 115 TYR 115 A LYS 116 n 116 LYS 116 A PRO 117 n 117 PRO 117 A ASN 118 n 118 ASN 118 A ASN 119 n 119 ASN 119 A THR 120 n 120 THR 120 A HIS 121 n 121 HIS 121 A GLU 122 n 122 GLU 122 A GLN 123 n 123 GLN 123 A HIS 124 n 124 HIS 124 A LEU 125 n 125 LEU 125 A ARG 126 n 126 ARG 126 A LYS 127 n 127 LYS 127 A SER 128 n 128 SER 128 A GLU 129 n 129 GLU 129 A ALA 130 n 130 ALA 130 A GLN 131 n 131 GLN 131 A ALA 132 n 132 ALA 132 A LYS 133 n 133 LYS 133 A LYS 134 n 134 LYS 134 A GLU 135 n 135 GLU 135 A LYS 136 n 136 LYS 136 A LEU 137 n 137 LEU 137 A ASN 138 n 138 ASN 138 A ILE 139 n 139 ILE 139 A TRP 140 n 140 TRP 140 A SER 141 n 141 SER 141 A n 142 142 A n 143 143 A n 144 144 A n 145 145 A n 146 146 A n 147 147 A n 148 148 A n 149 149 A author_defined_assembly 1 monomeric A ASP 21 A OD2 ASP 21 1_555 A CA 150 B CA CA 1_555 A ASP 40 A OD1 ASP 40 1_555 87.5 A ASP 21 A OD2 ASP 21 1_555 A CA 150 B CA CA 1_555 A THR 41 A O THR 41 1_555 88.7 A ASP 40 A OD1 ASP 40 1_555 A CA 150 B CA CA 1_555 A THR 41 A O THR 41 1_555 74.0 A ASP 21 A OD2 ASP 21 1_555 A CA 150 B CA CA 1_555 A THP 151 C O4P THP 1_555 101.4 A ASP 40 A OD1 ASP 40 1_555 A CA 150 B CA CA 1_555 A THP 151 C O4P THP 1_555 77.8 A THR 41 A O THR 41 1_555 A CA 150 B CA CA 1_555 A THP 151 C O4P THP 1_555 149.6 A ASP 21 A OD2 ASP 21 1_555 A CA 150 B CA CA 1_555 A HOH 209 D O HOH 1_555 83.2 A ASP 40 A OD1 ASP 40 1_555 A CA 150 B CA CA 1_555 A HOH 209 D O HOH 1_555 143.3 A THR 41 A O THR 41 1_555 A CA 150 B CA CA 1_555 A HOH 209 D O HOH 1_555 140.7 A THP 151 C O4P THP 1_555 A CA 150 B CA CA 1_555 A HOH 209 D O HOH 1_555 69.6 A ASP 21 A OD2 ASP 21 1_555 A CA 150 B CA CA 1_555 A HOH 229 D O HOH 1_555 85.1 A ASP 40 A OD1 ASP 40 1_555 A CA 150 B CA CA 1_555 A HOH 229 D O HOH 1_555 136.0 A THR 41 A O THR 41 1_555 A CA 150 B CA CA 1_555 A HOH 229 D O HOH 1_555 62.5 A THP 151 C O4P THP 1_555 A CA 150 B CA CA 1_555 A HOH 229 D O HOH 1_555 146.2 A HOH 209 D O HOH 1_555 A CA 150 B CA CA 1_555 A HOH 229 D O HOH 1_555 78.5 A ASP 21 A OD2 ASP 21 1_555 A CA 150 B CA CA 1_555 A HOH 245 D O HOH 1_555 173.9 A ASP 40 A OD1 ASP 40 1_555 A CA 150 B CA CA 1_555 A HOH 245 D O HOH 1_555 87.3 A THR 41 A O THR 41 1_555 A CA 150 B CA CA 1_555 A HOH 245 D O HOH 1_555 86.9 A THP 151 C O4P THP 1_555 A CA 150 B CA CA 1_555 A HOH 245 D O HOH 1_555 80.5 A HOH 209 D O HOH 1_555 A CA 150 B CA CA 1_555 A HOH 245 D O HOH 1_555 102.9 A HOH 229 D O HOH 1_555 A CA 150 B CA CA 1_555 A HOH 245 D O HOH 1_555 96.6 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 O GLU 10 A O GLU 10 A N VAL 74 A N VAL 74 A O GLU 73 A O GLU 73 A N TYR 93 A N TYR 93 A O GLY 88 A O GLY 88 A N ARG 35 A N ARG 35 A O GLN 30 A O GLN 30 A N TYR 27 A N TYR 27 A O LYS 24 A O LYS 24 A N LYS 16 A N LYS 16 A O ASP 40 A O ASP 40 A N LYS 110 A N LYS 110 1 A ALA 1 A ALA 1 1 Y 1 A THR 2 A THR 2 1 Y 1 A SER 3 A SER 3 1 Y 1 A THR 4 A THR 4 1 Y 1 A LYS 5 A LYS 5 1 Y 1 A LYS 6 A LYS 6 1 Y 1 A GLU 142 A GLU 142 1 Y 1 A ASP 143 A ASP 143 1 Y 1 A ASN 144 A ASN 144 1 Y 1 A ALA 145 A ALA 145 1 Y 1 A ASP 146 A ASP 146 1 Y 1 A SER 147 A SER 147 1 Y 1 A GLY 148 A GLY 148 1 Y 1 A GLN 149 A GLN 149 1 Y 1 A LYS 16 -170.68 132.90 1 A LYS 45 -100.57 -75.41 1 A TYR 54 83.15 -4.05 1 A ASN 119 -145.51 28.01 1 A ASN 138 36.82 -99.44 PARAM19X.PRO TOPH19X.PRO PARAM11.DNA 0.1730000 0.1730000 1.9 6.0 9359 1 2. MOLECULAR REPLACEMENT PDB ENTRY 1SNC 1.9 6.0 39 1146 26 0 1081 0.010 1.668 24.71 1.417 1.90 6.0 1NUC 9359 2. 0.0690000 1 10. 3.7 87.9 0.0720000 1.90 1.98 3. 3.0 76.5 model building X-PLOR 3.1 refinement X-PLOR 3.1 data reduction DENZO data scaling SCALEPACK phasing X-PLOR 3.1 STAPHYLOCOCCAL NUCLEASE, V23C VARIANT 1 N N 2 N N 3 N N 4 N N A GLY 55 A GLY 55 HELX_P A GLU 67 A GLU 67 1 1 13 A VAL 99 A VAL 99 HELX_P A GLN 106 A GLN 106 1 2 8 A GLU 122 A GLU 122 HELX_P A LYS 134 A LYS 134 1 3 13 metalc 2.468 A ASP 21 A OD2 ASP 21 1_555 A CA 150 B CA CA 1_555 metalc 2.364 A ASP 40 A OD1 ASP 40 1_555 A CA 150 B CA CA 1_555 metalc 2.776 A THR 41 A O THR 41 1_555 A CA 150 B CA CA 1_555 metalc 2.691 A CA 150 B CA CA 1_555 A THP 151 C O4P THP 1_555 metalc 2.293 A CA 150 B CA CA 1_555 A HOH 209 D O HOH 1_555 metalc 2.053 A CA 150 B CA CA 1_555 A HOH 229 D O HOH 1_555 metalc 1.544 A CA 150 B CA CA 1_555 A HOH 245 D O HOH 1_555 NUCLEASE NUCLEASE A LYS 116 A LYS 116 1 A PRO 117 A PRO 117 -0.06 NUC_STAAU UNP 1 1 P00644 MLVMTEYLLSAGICMAIVSILLIGMAISNVSKGQYAKRFFFFATSCLVLTLVVVSSLSSSANASQTDNGVNRSGSEDPTV YSATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDK GQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ 83 231 1NUC 1 149 P00644 A 1 1 149 1 VAL engineered mutation CYS 23 1NUC A P00644 UNP 105 23 6 2 anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel A LYS 9 A LYS 9 A ALA 12 A ALA 12 A ILE 72 A ILE 72 A PHE 76 A PHE 76 A GLY 88 A GLY 88 A ALA 94 A ALA 94 A GLN 30 A GLN 30 A LEU 36 A LEU 36 A THR 22 A THR 22 A TYR 27 A TYR 27 A THR 13 A THR 13 A ALA 17 A ALA 17 A VAL 39 A VAL 39 A THR 41 A THR 41 A ALA 109 A ALA 109 A VAL 111 A VAL 111 BINDING SITE FOR RESIDUE CA A 150 A CA 150 Software 7 BINDING SITE FOR RESIDUE THP A 151 A THP 151 Software 16 A ASP 21 A ASP 21 7 1_555 A ASP 40 A ASP 40 7 1_555 A THR 41 A THR 41 7 1_555 A THP 151 C THP 7 1_555 A HOH 209 D HOH 7 1_555 A HOH 229 D HOH 7 1_555 A HOH 245 D HOH 7 1_555 A ARG 35 A ARG 35 16 1_555 A ASP 40 A ASP 40 16 1_555 A LYS 71 A LYS 71 16 3_655 A LYS 84 A LYS 84 16 1_555 A TYR 85 A TYR 85 16 1_555 A ARG 87 A ARG 87 16 1_555 A LEU 89 A LEU 89 16 1_555 A TYR 113 A TYR 113 16 1_555 A TYR 115 A TYR 115 16 1_555 A CA 150 B CA 16 1_555 A HOH 202 D HOH 16 3_555 A HOH 209 D HOH 16 1_555 A HOH 217 D HOH 16 1_555 A HOH 218 D HOH 16 1_555 A HOH 226 D HOH 16 1_555 A HOH 245 D HOH 16 1_555 76 P 41