1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Hasegawa, J. Yoshida, T. Yamazaki, T. Sambongi, Y. Yu, Y. Igarashi, Y. Kodama, T. Yamazaki, K. Hakusui, H. Kyogoku, Y. Kobayashi, Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 H34 Fe N4 O4 618.503 HEME C non-polymer C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking 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 C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide 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 Biochemistry BICHAW 0033 0006-2960 37 9641 9649 10.1021/bi9803067 9657676 Solution structure of thermostable cytochrome c-552 from Hydrogenobacter thermophilus determined by 1H-NMR spectroscopy. 1998 10.2210/pdb1ayg/pdb pdb_00001ayg 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 C-TYPE CYTOCHROME (REDUCED FORM) 8586.015 CYTOCHROME C-552 1 nat polymer 618.503 HEME C 1 syn non-polymer no no NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK 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 Hydrogenobacter sample PERIPLASM 940 Hydrogenobacter thermophilus TK-6 database_2 pdbx_database_status pdbx_nmr_exptl_sample_conditions pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Experimental preparation Other 1 0 1998-11-25 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_nmr_exptl_sample_conditions.pressure_units _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_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1997-11-04 REL HEC HEME C THE STRUCTURE WAS DETERMINED USING 1H-NMR SPECTROSCOPY ON CYTOCHROME C-552 LOWER ENERGY 100 20 NOESY DQF-COSY TOCSY E.COSY 120mM ACETATE 4.8 1 atm 298 K SIMULATED ANNEALING REFINEMENT FOR NMR STRUCTURE DETERMINATION. simulated annealing 90% H2O/10% D2O, OR 99.98% D2O CONTAINING 120MM DEUTERATED ACETATE BUFFER BRUNGER refinement X-PLOR 3.1 structure solution X-PLOR 500 Bruker ARX500 750 Bruker AMX500 & DMX750 HEC 81 2 HEC HEC 81 A ASN 1 n 1 ASN 1 A GLU 2 n 2 GLU 2 A GLN 3 n 3 GLN 3 A LEU 4 n 4 LEU 4 A ALA 5 n 5 ALA 5 A LYS 6 n 6 LYS 6 A GLN 7 n 7 GLN 7 A LYS 8 n 8 LYS 8 A GLY 9 n 9 GLY 9 A CYS 10 n 10 CYS 10 A MET 11 n 11 MET 11 A ALA 12 n 12 ALA 12 A CYS 13 n 13 CYS 13 A HIS 14 n 14 HIS 14 A ASP 15 n 15 ASP 15 A LEU 16 n 16 LEU 16 A LYS 17 n 17 LYS 17 A ALA 18 n 18 ALA 18 A LYS 19 n 19 LYS 19 A LYS 20 n 20 LYS 20 A VAL 21 n 21 VAL 21 A GLY 22 n 22 GLY 22 A PRO 23 n 23 PRO 23 A ALA 24 n 24 ALA 24 A TYR 25 n 25 TYR 25 A ALA 26 n 26 ALA 26 A ASP 27 n 27 ASP 27 A VAL 28 n 28 VAL 28 A ALA 29 n 29 ALA 29 A LYS 30 n 30 LYS 30 A LYS 31 n 31 LYS 31 A TYR 32 n 32 TYR 32 A ALA 33 n 33 ALA 33 A GLY 34 n 34 GLY 34 A ARG 35 n 35 ARG 35 A LYS 36 n 36 LYS 36 A ASP 37 n 37 ASP 37 A ALA 38 n 38 ALA 38 A VAL 39 n 39 VAL 39 A ASP 40 n 40 ASP 40 A TYR 41 n 41 TYR 41 A LEU 42 n 42 LEU 42 A ALA 43 n 43 ALA 43 A GLY 44 n 44 GLY 44 A LYS 45 n 45 LYS 45 A ILE 46 n 46 ILE 46 A LYS 47 n 47 LYS 47 A LYS 48 n 48 LYS 48 A GLY 49 n 49 GLY 49 A GLY 50 n 50 GLY 50 A SER 51 n 51 SER 51 A GLY 52 n 52 GLY 52 A VAL 53 n 53 VAL 53 A TRP 54 n 54 TRP 54 A GLY 55 n 55 GLY 55 A SER 56 n 56 SER 56 A VAL 57 n 57 VAL 57 A PRO 58 n 58 PRO 58 A MET 59 n 59 MET 59 A PRO 60 n 60 PRO 60 A PRO 61 n 61 PRO 61 A GLN 62 n 62 GLN 62 A ASN 63 n 63 ASN 63 A VAL 64 n 64 VAL 64 A THR 65 n 65 THR 65 A ASP 66 n 66 ASP 66 A ALA 67 n 67 ALA 67 A GLU 68 n 68 GLU 68 A ALA 69 n 69 ALA 69 A LYS 70 n 70 LYS 70 A GLN 71 n 71 GLN 71 A LEU 72 n 72 LEU 72 A ALA 73 n 73 ALA 73 A GLN 74 n 74 GLN 74 A TRP 75 n 75 TRP 75 A ILE 76 n 76 ILE 76 A LEU 77 n 77 LEU 77 A SER 78 n 78 SER 78 A ILE 79 n 79 ILE 79 A LYS 80 n 80 LYS 80 A author_defined_assembly 1 monomeric A HIS 14 A NE2 HIS 14 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B NA HEC 1_555 72.8 A HIS 14 A NE2 HIS 14 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B NB HEC 1_555 105.3 A HEC 81 B NA HEC 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B NB HEC 1_555 90.0 A HIS 14 A NE2 HIS 14 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B NC HEC 1_555 105.8 A HEC 81 B NA HEC 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B NC HEC 1_555 178.5 A HEC 81 B NB HEC 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B NC HEC 1_555 90.0 A HIS 14 A NE2 HIS 14 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B ND HEC 1_555 74.4 A HEC 81 B NA HEC 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B ND HEC 1_555 90.2 A HEC 81 B NB HEC 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B ND HEC 1_555 179.7 A HEC 81 B NC HEC 1_555 A HEC 81 B FE HEC 1_555 A HEC 81 B ND HEC 1_555 89.9 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 1 A GLU 2 -157.07 -41.75 1 A ASP 15 163.63 148.74 1 A LEU 16 -50.39 -75.68 1 A ALA 18 -118.39 67.58 1 A LYS 20 -128.96 -95.72 1 A VAL 21 -94.27 -72.81 1 A ALA 33 163.59 109.91 1 A LEU 42 -56.78 -70.87 1 A LYS 48 -129.79 -59.97 1 A SER 51 179.50 167.65 1 A ASN 63 -104.09 78.07 2 A GLU 2 -178.69 -40.08 2 A ASP 15 161.07 136.12 2 A LYS 20 -140.39 -56.46 2 A TYR 32 -109.94 -132.57 2 A ALA 33 78.50 107.67 2 A ASP 37 -94.27 39.08 2 A LEU 42 -65.14 -70.09 2 A SER 51 169.49 56.50 2 A VAL 57 -50.01 106.98 3 A GLN 3 173.06 -42.62 3 A HIS 14 -108.39 -169.38 3 A ASP 15 162.69 135.95 3 A TYR 32 -96.61 -115.57 3 A ALA 33 76.66 106.97 3 A ASN 63 -104.57 57.22 4 A GLN 3 82.73 -43.29 4 A HIS 14 -69.87 -171.39 4 A ASP 15 169.98 132.28 4 A LEU 16 -42.65 -70.05 4 A ALA 18 -153.70 59.46 4 A LYS 19 -48.92 101.79 4 A ALA 33 170.47 -32.81 4 A VAL 57 -46.17 104.60 4 A ASN 63 -96.32 55.15 5 A GLN 3 168.65 -75.29 5 A ASP 15 -160.44 23.27 5 A LEU 16 81.36 -59.32 5 A LYS 19 -51.17 97.09 5 A LYS 20 -113.16 -89.37 5 A ILE 46 -102.20 -60.03 5 A SER 51 179.81 150.76 5 A VAL 57 -43.66 107.61 5 A GLN 62 -100.46 -162.79 5 A ASN 63 -117.69 65.84 5 A ILE 79 -47.85 100.05 6 A GLU 2 -176.41 -44.20 6 A LYS 6 -88.92 -73.75 6 A ASP 15 -178.94 139.66 6 A ALA 18 53.86 109.01 6 A LYS 19 172.91 59.71 6 A LYS 20 -171.65 -176.19 6 A ALA 24 -49.73 153.23 6 A ALA 33 168.61 107.93 6 A ASP 37 -174.86 50.31 6 A LYS 48 -159.35 64.57 6 A VAL 57 -48.35 109.99 7 A GLU 2 -113.10 71.60 7 A GLN 3 -175.11 -47.69 7 A CYS 13 -131.64 -39.37 7 A HIS 14 -74.87 -168.63 7 A ASP 15 166.86 136.15 7 A LYS 19 -42.64 100.66 7 A VAL 21 -126.96 -68.67 7 A TYR 32 -112.39 -127.55 7 A ALA 33 80.35 108.00 7 A LYS 48 -142.25 11.77 7 A SER 51 174.74 94.92 7 A ASN 63 -97.33 58.87 7 A ILE 79 -62.06 99.72 8 A GLN 3 84.04 -25.75 8 A GLN 7 -56.75 -74.77 8 A ASP 15 162.78 123.16 8 A ALA 18 -164.35 49.96 8 A LYS 19 -49.49 164.94 8 A LYS 20 -150.09 -65.10 8 A TYR 32 -107.71 -139.96 8 A ALA 33 83.37 112.80 8 A LYS 48 -108.03 -77.46 8 A SER 51 179.02 156.20 8 A TRP 54 -134.08 -30.71 8 A ASN 63 -110.53 72.77 9 A GLN 3 -142.82 -43.31 9 A ASP 15 166.99 120.68 9 A ALA 18 -152.78 72.43 9 A LYS 20 -116.59 -77.13 9 A ALA 33 160.78 109.78 9 A LYS 48 -144.23 31.42 9 A SER 51 174.89 90.98 9 A VAL 57 -41.56 101.70 9 A ILE 79 -69.79 92.11 10 A GLU 2 -171.32 -40.93 10 A CYS 13 -133.45 -40.04 10 A ASP 15 163.47 119.37 10 A LYS 20 -142.16 -69.43 10 A TYR 32 -104.38 -149.87 10 A ALA 33 84.10 -33.73 10 A LYS 36 -96.88 33.68 10 A ASP 37 169.66 45.18 10 A LYS 48 -123.33 -71.70 10 A SER 51 177.22 144.18 11 A ASP 15 164.39 129.02 11 A LYS 20 -160.26 -97.05 11 A TYR 32 -125.64 -145.57 11 A ALA 33 81.92 109.82 11 A ARG 35 -82.97 36.92 11 A LYS 36 69.73 -4.70 11 A ASP 37 167.05 52.87 11 A LEU 42 -47.13 -75.90 11 A SER 51 168.27 81.80 11 A ASN 63 -88.67 47.16 12 A GLU 2 -179.57 -34.78 12 A ASP 15 173.19 136.25 12 A ALA 18 -152.73 81.32 12 A LYS 19 -55.16 90.50 12 A LYS 20 -89.97 -156.52 12 A TYR 32 -98.27 -101.89 12 A ALA 33 72.37 104.97 12 A SER 51 -173.65 143.32 12 A ASN 63 -102.15 60.98 13 A GLN 3 169.95 -44.77 13 A ASP 15 -176.80 145.77 13 A ALA 18 55.39 -179.29 13 A LYS 19 70.53 101.72 13 A LYS 20 167.22 -166.65 13 A TYR 32 -104.37 -111.63 13 A ALA 33 75.07 105.63 13 A LYS 48 -111.80 -76.88 13 A ASN 63 -115.86 76.00 14 A GLU 2 -118.77 75.67 14 A GLN 3 -157.47 -55.22 14 A ASP 15 162.74 135.01 14 A LYS 20 -131.56 -95.80 14 A ALA 24 -49.93 155.84 14 A SER 51 177.87 84.26 14 A TRP 54 -144.83 35.63 14 A VAL 57 -43.30 103.61 15 A GLU 2 49.26 85.24 15 A GLN 3 -170.66 -62.31 15 A HIS 14 -62.09 -174.86 15 A ASP 15 170.70 127.11 15 A LEU 16 -42.36 -71.73 15 A LYS 20 -91.71 -74.46 15 A TYR 32 -88.94 -103.50 15 A ALA 33 75.40 106.98 15 A LYS 48 -126.71 -78.84 16 A GLN 3 -170.05 -37.32 16 A GLN 7 -53.92 -79.35 16 A ASP 15 166.69 136.23 16 A LYS 19 -61.47 98.26 16 A LYS 20 -109.07 -97.76 16 A TYR 32 -123.64 -144.42 16 A ALA 33 78.96 107.46 16 A ARG 35 -61.06 -163.66 16 A ASP 37 178.77 70.86 16 A SER 51 176.04 159.57 16 A VAL 57 -46.38 106.62 17 A GLN 3 179.74 -48.94 17 A ASP 15 164.29 124.02 17 A ALA 18 -158.10 58.56 17 A LYS 20 -122.81 -105.45 17 A TYR 32 -106.55 -143.63 17 A ALA 33 83.55 -37.70 17 A ASP 37 -178.85 44.92 17 A LYS 48 -104.25 -72.68 18 A GLU 2 -165.30 62.94 18 A GLN 3 -172.25 -49.42 18 A LYS 6 -54.78 -71.74 18 A ASP 15 164.68 126.61 18 A LYS 19 -53.02 108.97 18 A LYS 20 -114.06 -147.20 18 A TYR 32 -106.88 -142.65 18 A ALA 33 80.98 107.38 18 A LYS 48 -125.01 -66.70 18 A SER 56 -113.16 51.60 18 A ASN 63 -109.34 52.07 19 A GLU 2 179.93 42.30 19 A ASP 15 175.58 137.21 19 A ALA 18 49.31 98.34 19 A LYS 19 171.04 88.34 19 A LYS 20 175.26 -153.31 19 A TYR 32 -101.44 -123.44 19 A ALA 33 81.24 109.95 19 A LYS 48 -149.18 -71.67 19 A SER 51 179.25 143.57 19 A TRP 54 -152.66 33.15 19 A ASN 63 -98.86 50.07 20 A GLU 2 46.34 86.40 20 A GLN 3 179.17 -54.21 20 A ASP 15 164.06 147.94 20 A ALA 18 -140.44 55.10 20 A LYS 20 -122.52 -91.39 20 A ALA 33 175.32 107.80 20 A LYS 48 -146.66 -46.19 20 A SER 56 -95.61 41.72 20 A GLN 62 -118.86 -166.62 20 A ASN 63 -113.19 77.62 model building X-PLOR 3.1 refinement X-PLOR 3.1 phasing X-PLOR 3.1 SOLUTION STRUCTURE OF CYTOCHROME C-552, NMR, 20 STRUCTURES 1 Y N 2 N N A GLN 3 A GLN 3 HELX_P A GLN 7 A GLN 7 1 1 5 A TYR 25 A TYR 25 HELX_P A TYR 32 A TYR 32 1 2 8 A ALA 38 A ALA 38 HELX_P A LYS 47 A LYS 47 1 3 10 A ALA 67 A ALA 67 HELX_P A SER 78 A SER 78 1 4 12 covale 1.812 none A CYS 10 A SG CYS 10 1_555 A HEC 81 B CAB HEC 1_555 covale 1.813 none A CYS 13 A SG CYS 13 1_555 A HEC 81 B CAC HEC 1_555 metalc 2.984 A HIS 14 A NE2 HIS 14 1_555 A HEC 81 B FE HEC 1_555 ELECTRON TRANSPORT CYTOCHROME C, ELECTRON TRANSPORT, PORPHYRIN, FERROUS IRON CY552_HYDTH UNP 1 1 P15452 MKKFLLVAVVGLAGITFANEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQ NVTDAEAKQLAQWILSIK 19 98 1AYG 1 80 P15452 A 1 1 80 BINDING SITE FOR RESIDUE HEC A 81 A HEC 81 Software 14 A GLY 9 A GLY 9 14 1_555 A CYS 10 A CYS 10 14 1_555 A CYS 13 A CYS 13 14 1_555 A HIS 14 A HIS 14 14 1_555 A PRO 23 A PRO 23 14 1_555 A TYR 32 A TYR 32 14 1_555 A ILE 46 A ILE 46 14 1_555 A GLY 52 A GLY 52 14 1_555 A TRP 54 A TRP 54 14 1_555 A GLY 55 A GLY 55 14 1_555 A VAL 57 A VAL 57 14 1_555 A MET 59 A MET 59 14 1_555 A GLN 62 A GLN 62 14 1_555 A LEU 72 A LEU 72 14 1_555 1 P 1