0.027382 0.000000 0.000000 0.000000 0.027382 0.000000 0.000000 0.000000 0.007279 0.00000 0.00000 0.00000 Berghuis, A.M. Brayer, G.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 36.520 36.520 137.390 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 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 C34 H32 Fe N4 O4 616.487 PROTOPORPHYRIN IX CONTAINING FE HEME non-polymer 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 H21 N2 O2 1 189.275 n N-TRIMETHYLLYSINE 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 O4 S -2 96.063 SULFATE ION 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 Biochemistry BICHAW 0033 0006-2960 35 10784 10792 10.1021/bi960430v 8718869 Mechanistic and structural contributions of critical surface and internal residues to cytochrome c electron transfer reactivity. 1996 UK J.Mol.Biol. JMOBAK 0070 0022-2836 236 786 The Role of a Conserved Internal Water Molecule and its Associated Hydrogen Bond Network in Cytochrome C 1994 UK J.Mol.Biol. JMOBAK 0070 0022-2836 235 1326 Mutation of Tyrosine-67 to Phenylalanine in Cytochrome C Significantly Alters the Local Heme Environment 1994 UK J.Mol.Biol. JMOBAK 0070 0022-2836 223 959 Oxidation State-Dependent Conformational Changes in Cytochrome C 1992 UK J.Mol.Biol. JMOBAK 0070 0022-2836 214 527 High-Resolution Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochromes C 1990 UK J.Mol.Biol. JMOBAK 0070 0022-2836 206 783 Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique 1989 10.2210/pdb1irw/pdb pdb_00001irw 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 DIFFRACTOMETER 1992 ENRAF-NONIUS FAST M x-ray 1 1.5418 1.0 1.5418 ISOZYME 1, REDUCED 12070.851 CYTOCHROME C N52A, C102T 1 man polymer 96.063 SULFATE ION 1 syn non-polymer 616.487 PROTOPORPHYRIN IX CONTAINING FE 1 syn non-polymer 18.015 water 48 nat water no yes TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDAAIKKNVLWDENNMSEYLTNP (M3L)KYIPGTKMAFGGLKKEKDRNDLITYLKKATE TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDAAIKKNVLWDENNMSEYLTNPKKYI PGTKMAFGGLKKEKDRNDLITYLKKATE 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 baker's yeast Saccharomyces sample 4932 Saccharomyces cerevisiae 1.90 35.16 pdbx_database_status struct_conf struct_conf_type diffrn_detector database_2 struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Derived calculations Other Data collection Database references Derived calculations 1 0 1997-01-11 1 1 2008-03-24 1 2 2011-07-13 1 3 2017-11-29 1 4 2018-04-18 1 5 2021-11-03 _pdbx_database_status.process_site _diffrn_detector.detector _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _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 1996-06-27 REL REL SO4 SULFATE ION HEM PROTOPORPHYRIN IX CONTAINING FE HOH water SO4 117 2 SO4 SO4 117 A HEM 104 3 HEM HEM 104 A HOH 106 4 HOH HOH 106 A HOH 107 4 HOH HOH 107 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 119 4 HOH HOH 119 A HOH 121 4 HOH HOH 121 A HOH 122 4 HOH HOH 122 A HOH 128 4 HOH HOH 128 A HOH 129 4 HOH HOH 129 A HOH 131 4 HOH HOH 131 A HOH 133 4 HOH HOH 133 A HOH 140 4 HOH HOH 140 A HOH 141 4 HOH HOH 141 A HOH 144 4 HOH HOH 144 A HOH 148 4 HOH HOH 148 A HOH 149 4 HOH HOH 149 A HOH 150 4 HOH HOH 150 A HOH 153 4 HOH HOH 153 A HOH 156 4 HOH HOH 156 A HOH 158 4 HOH HOH 158 A HOH 160 4 HOH HOH 160 A HOH 163 4 HOH HOH 163 A HOH 164 4 HOH HOH 164 A HOH 166 4 HOH HOH 166 A HOH 167 4 HOH HOH 167 A HOH 168 4 HOH HOH 168 A HOH 181 4 HOH HOH 181 A HOH 182 4 HOH HOH 182 A HOH 183 4 HOH HOH 183 A HOH 195 4 HOH HOH 195 A HOH 197 4 HOH HOH 197 A HOH 204 4 HOH HOH 204 A HOH 209 4 HOH HOH 209 A HOH 214 4 HOH HOH 214 A HOH 300 4 HOH HOH 300 A HOH 301 4 HOH HOH 301 A HOH 302 4 HOH HOH 302 A HOH 303 4 HOH HOH 303 A HOH 304 4 HOH HOH 304 A HOH 305 4 HOH HOH 305 A HOH 306 4 HOH HOH 306 A HOH 307 4 HOH HOH 307 A HOH 308 4 HOH HOH 308 A HOH 309 4 HOH HOH 309 A HOH 310 4 HOH HOH 310 A HOH 311 4 HOH HOH 311 A THR -5 n 1 THR -5 A GLU -4 n 2 GLU -4 A PHE -3 n 3 PHE -3 A LYS -2 n 4 LYS -2 A ALA -1 n 5 ALA -1 A GLY 1 n 6 GLY 1 A SER 2 n 7 SER 2 A ALA 3 n 8 ALA 3 A LYS 4 n 9 LYS 4 A LYS 5 n 10 LYS 5 A GLY 6 n 11 GLY 6 A ALA 7 n 12 ALA 7 A THR 8 n 13 THR 8 A LEU 9 n 14 LEU 9 A PHE 10 n 15 PHE 10 A LYS 11 n 16 LYS 11 A THR 12 n 17 THR 12 A ARG 13 n 18 ARG 13 A CYS 14 n 19 CYS 14 A LEU 15 n 20 LEU 15 A GLN 16 n 21 GLN 16 A CYS 17 n 22 CYS 17 A HIS 18 n 23 HIS 18 A THR 19 n 24 THR 19 A VAL 20 n 25 VAL 20 A GLU 21 n 26 GLU 21 A LYS 22 n 27 LYS 22 A GLY 23 n 28 GLY 23 A GLY 24 n 29 GLY 24 A PRO 25 n 30 PRO 25 A HIS 26 n 31 HIS 26 A LYS 27 n 32 LYS 27 A VAL 28 n 33 VAL 28 A GLY 29 n 34 GLY 29 A PRO 30 n 35 PRO 30 A ASN 31 n 36 ASN 31 A LEU 32 n 37 LEU 32 A HIS 33 n 38 HIS 33 A GLY 34 n 39 GLY 34 A ILE 35 n 40 ILE 35 A PHE 36 n 41 PHE 36 A GLY 37 n 42 GLY 37 A ARG 38 n 43 ARG 38 A HIS 39 n 44 HIS 39 A SER 40 n 45 SER 40 A GLY 41 n 46 GLY 41 A GLN 42 n 47 GLN 42 A ALA 43 n 48 ALA 43 A GLU 44 n 49 GLU 44 A GLY 45 n 50 GLY 45 A TYR 46 n 51 TYR 46 A SER 47 n 52 SER 47 A TYR 48 n 53 TYR 48 A THR 49 n 54 THR 49 A ASP 50 n 55 ASP 50 A ALA 51 n 56 ALA 51 A ALA 52 n 57 ALA 52 A ILE 53 n 58 ILE 53 A LYS 54 n 59 LYS 54 A LYS 55 n 60 LYS 55 A ASN 56 n 61 ASN 56 A VAL 57 n 62 VAL 57 A LEU 58 n 63 LEU 58 A TRP 59 n 64 TRP 59 A ASP 60 n 65 ASP 60 A GLU 61 n 66 GLU 61 A ASN 62 n 67 ASN 62 A ASN 63 n 68 ASN 63 A MET 64 n 69 MET 64 A SER 65 n 70 SER 65 A GLU 66 n 71 GLU 66 A TYR 67 n 72 TYR 67 A LEU 68 n 73 LEU 68 A THR 69 n 74 THR 69 A ASN 70 n 75 ASN 70 A PRO 71 n 76 PRO 71 A M3L 72 n 77 M3L 72 A LYS 73 n 78 LYS 73 A TYR 74 n 79 TYR 74 A ILE 75 n 80 ILE 75 A PRO 76 n 81 PRO 76 A GLY 77 n 82 GLY 77 A THR 78 n 83 THR 78 A LYS 79 n 84 LYS 79 A MET 80 n 85 MET 80 A ALA 81 n 86 ALA 81 A PHE 82 n 87 PHE 82 A GLY 83 n 88 GLY 83 A GLY 84 n 89 GLY 84 A LEU 85 n 90 LEU 85 A LYS 86 n 91 LYS 86 A LYS 87 n 92 LYS 87 A GLU 88 n 93 GLU 88 A LYS 89 n 94 LYS 89 A ASP 90 n 95 ASP 90 A ARG 91 n 96 ARG 91 A ASN 92 n 97 ASN 92 A ASP 93 n 98 ASP 93 A LEU 94 n 99 LEU 94 A ILE 95 n 100 ILE 95 A THR 96 n 101 THR 96 A TYR 97 n 102 TYR 97 A LEU 98 n 103 LEU 98 A LYS 99 n 104 LYS 99 A LYS 100 n 105 LYS 100 A ALA 101 n 106 ALA 101 A THR 102 n 107 THR 102 A GLU 103 n 108 GLU 103 A author_defined_assembly 1 monomeric A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NA HEM 1_555 86.1 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NB HEM 1_555 89.3 A HEM 104 C NA HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NB HEM 1_555 91.6 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NC HEM 1_555 85.6 A HEM 104 C NA HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NC HEM 1_555 171.7 A HEM 104 C NB HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NC HEM 1_555 89.3 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C ND HEM 1_555 86.2 A HEM 104 C NA HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C ND HEM 1_555 89.2 A HEM 104 C NB HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C ND HEM 1_555 175.3 A HEM 104 C NC HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C ND HEM 1_555 89.2 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 178.7 A HEM 104 C NA HEM 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 94.4 A HEM 104 C NB HEM 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 91.8 A HEM 104 C NC HEM 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 93.8 A HEM 104 C ND HEM 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 92.7 A M3L 72 N-TRIMETHYLLYSINE A M3L 77 LYS 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 SER 40 A N SER 45 A O VAL 57 A O VAL 62 1 9.15 1.50 110.90 120.05 A A A CA CB CG1 VAL VAL VAL 20 20 20 N 1 6.67 0.50 120.30 126.97 A A A NE CZ NH1 ARG ARG ARG 38 38 38 N 1 15.37 2.20 113.40 128.77 A A A CA CB CG GLU GLU GLU 44 44 44 N 1 -4.07 0.60 121.00 116.93 A A A CB CG CD1 TYR TYR TYR 74 74 74 N 1 10.67 1.60 122.70 133.37 A A A O C N MET MET ALA 80 80 81 Y 1 -6.61 0.90 118.30 111.69 A A A CB CG OD2 ASP ASP ASP 90 90 90 N 1 3.66 0.50 120.30 123.96 A A A NE CZ NH2 ARG ARG ARG 91 91 91 N 1 A GLU -4 -162.33 0.91 1 A LYS 27 -123.84 -119.99 1 A ASN 70 -167.73 88.66 17.9 PROLSQ STANDARD SET OF IDEAL BOND LENGTHS ETC. (I.E. VERY SIMILAR TO ENGH & HUBER) ESTIMATED COORD. ERROR 0.18 ANGSTROMS FINAL RMS COORD. SHIFT 0.27 ANGSTROMS 0.1830000 2.0 6.0 4146 1 2.0 0.20 2.0 6.0 48 944 48 0 848 0.020 0.020 0.044 0.030 0.052 0.050 1.630 1.500 2.422 2.500 2.383 2.000 3.617 3.000 0.016 0.020 0.196 0.150 0.219 0.250 0.207 0.250 0.245 0.250 2.6 2.5 25.9 19.0 19.1 15.0 2.0 1IRW 6933 0.0 1 1. 100. refinement PROLSQ data reduction IN-HOUSE SOFTWARE CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ASN 52 REPLACED BY ALA AND CYS 102 REPLACED BY THR 1 N N 2 N N 3 N N 4 N N A ALA 3 A ALA 8 HELX_P A ARG 13 A ARG 18 1 1 11 A ASP 50 A ASP 55 HELX_P A LYS 55 A LYS 60 1 2 6 A GLU 61 A GLU 66 HELX_P A THR 69 A THR 74 1 3 9 A PRO 71 A PRO 76 HELX_P A TYR 74 A TYR 79 5 4 4 A GLU 88 A GLU 93 HELX_P A ALA 101 A ALA 106 1 5 14 covale 1.744 none A CYS 14 A SG CYS 19 1_555 A HEM 104 C CAB HEM 1_555 covale 1.833 none A CYS 17 A SG CYS 22 1_555 A HEM 104 C CAC HEM 1_555 covale 1.331 both A PRO 71 A C PRO 76 1_555 A M3L 72 A N M3L 77 1_555 covale 1.284 both A M3L 72 A C M3L 77 1_555 A LYS 73 A N LYS 78 1_555 metalc 2.001 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 metalc 2.286 A MET 80 A SD MET 85 1_555 A HEM 104 C FE HEM 1_555 ELECTRON TRANSPORT HEME PROTEIN, MITOCHONDRION, ELECTRON TRANSPORT CYC1_YEAST UNP 1 1 P00044 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYI PGTKMAFGGLKKEKDRNDLITYLKKACE 1 108 1IRW -5 103 P00044 A 1 1 108 1 ASN engineered mutation ALA 52 1IRW A P00044 UNP 57 57 1 LYS modified residue M3L 72 1IRW A P00044 UNP 77 77 1 CYS engineered mutation THR 102 1IRW A P00044 UNP 107 107 2 anti-parallel A GLY 37 A GLY 42 A SER 40 A SER 45 A VAL 57 A VAL 62 A TRP 59 A TRP 64 BINDING SITE FOR RESIDUE SO4 A 117 A SO4 117 Software 4 BINDING SITE FOR RESIDUE HEM A 104 A HEM 104 Software 19 A SER 2 A SER 7 4 1_555 A ALA 3 A ALA 8 4 1_555 A LYS 4 A LYS 9 4 1_555 A SER 47 A SER 52 4 3_554 A ARG 13 A ARG 18 19 1_555 A CYS 14 A CYS 19 19 1_555 A CYS 17 A CYS 22 19 1_555 A HIS 18 A HIS 23 19 1_555 A GLY 23 A GLY 28 19 6_465 A VAL 28 A VAL 33 19 1_555 A ILE 35 A ILE 40 19 1_555 A SER 40 A SER 45 19 1_555 A GLY 41 A GLY 46 19 1_555 A TYR 46 A TYR 51 19 1_555 A TYR 48 A TYR 53 19 1_555 A THR 49 A THR 54 19 1_555 A TRP 59 A TRP 64 19 1_555 A MET 64 A MET 69 19 1_555 A THR 78 A THR 83 19 1_555 A LYS 79 A LYS 84 19 1_555 A MET 80 A MET 85 19 1_555 A PHE 82 A PHE 87 19 1_555 A HOH 121 D HOH 19 1_555 96 P 43 21 2