0.015100 0.008718 0.000000 0.000000 0.017436 0.000000 0.000000 0.000000 0.024654 0.00000 0.00000 0.00000 Genick, U.K. Soltis, S.M. Kuhn, P. Canestrelli, I.L. Getzoff, E.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 66.224 66.224 40.561 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 C9 H8 O3 164.158 4'-HYDROXYCINNAMIC ACID PARA-COUMARIC ACID 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 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 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 UK Nature NATUAS 0006 0028-0836 392 206 209 10.1038/32462 9515969 Structure at 0.85 A resolution of an early protein photocycle intermediate. 1998 10.2210/pdb3pyp/pdb pdb_00003pyp 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 149 1 MIRRORS IMAGE PLATE 1997-09-06 MARRESEARCH SI(111) M x-ray 1 0.77 1.0 BL9-1 SSRL 0.77 SYNCHROTRON SSRL BEAMLINE BL9-1 THIOESTER LINKAGE BETWEEN THE SULFUR OF CYS 69 AND CARBOXY GROUP OF THE 4-HYDROXY CINNAMIC ACID CHROMOPHORE 13888.575 PHOTOACTIVE YELLOW PROTEIN 1 nat polymer 164.158 4'-HYDROXYCINNAMIC ACID 1 syn non-polymer 18.015 water 137 nat water PYP no no MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV 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 Halorhodospira sample 1053 Halorhodospira halophila BN9626 1 1.8 32 CRYSTALS IDENTICAL TO 2PHY 4.8 pH 4.8 pdbx_database_status struct_conf struct_conf_type database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Version format compliance Version format compliance Derived calculations Other Database references Derived calculations Refinement description 1 0 1999-06-01 1 1 2008-03-25 1 2 2011-07-13 1 3 2017-11-29 1 4 2023-08-09 _pdbx_database_status.process_site _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 1998-07-28 REL REL HC4 4'-HYDROXYCINNAMIC ACID HOH water 2PHY PDB experimental model HC4 69 2 HC4 HC4 126 A HOH 1001 3 HOH HOH 1001 A HOH 1002 3 HOH HOH 1002 A HOH 1003 3 HOH HOH 1003 A HOH 1004 3 HOH HOH 1004 A HOH 1005 3 HOH HOH 1005 A HOH 1006 3 HOH HOH 1006 A HOH 1007 3 HOH HOH 1007 A HOH 1008 3 HOH HOH 1008 A HOH 1009 3 HOH HOH 1009 A HOH 1010 3 HOH HOH 1010 A HOH 1011 3 HOH HOH 1011 A HOH 1012 3 HOH HOH 1012 A HOH 1013 3 HOH HOH 1013 A HOH 1014 3 HOH HOH 1014 A HOH 1015 3 HOH HOH 1015 A HOH 1016 3 HOH HOH 1016 A HOH 1017 3 HOH HOH 1017 A HOH 1018 3 HOH HOH 1018 A HOH 1019 3 HOH HOH 1019 A HOH 1020 3 HOH HOH 1020 A HOH 1021 3 HOH HOH 1021 A HOH 1022 3 HOH HOH 1022 A HOH 1023 3 HOH HOH 1023 A HOH 1024 3 HOH HOH 1024 A HOH 1025 3 HOH HOH 1025 A HOH 1026 3 HOH HOH 1026 A HOH 1027 3 HOH HOH 1027 A HOH 1028 3 HOH HOH 1028 A HOH 1029 3 HOH HOH 1029 A HOH 1030 3 HOH HOH 1030 A HOH 1031 3 HOH HOH 1031 A HOH 1032 3 HOH HOH 1032 A HOH 1033 3 HOH HOH 1033 A HOH 1034 3 HOH HOH 1034 A HOH 1035 3 HOH HOH 1035 A HOH 1036 3 HOH HOH 1036 A HOH 1038 3 HOH HOH 1038 A HOH 1039 3 HOH HOH 1039 A HOH 1040 3 HOH HOH 1040 A HOH 1041 3 HOH HOH 1041 A HOH 1042 3 HOH HOH 1042 A HOH 1043 3 HOH HOH 1043 A HOH 1044 3 HOH HOH 1044 A HOH 1045 3 HOH HOH 1045 A HOH 1046 3 HOH HOH 1046 A HOH 1048 3 HOH HOH 1048 A HOH 1049 3 HOH HOH 1049 A HOH 1050 3 HOH HOH 1050 A HOH 1051 3 HOH HOH 1051 A HOH 1054 3 HOH HOH 1054 A HOH 1055 3 HOH HOH 1055 A HOH 1056 3 HOH HOH 1056 A HOH 1057 3 HOH HOH 1057 A HOH 1059 3 HOH HOH 1059 A HOH 1060 3 HOH HOH 1060 A HOH 1061 3 HOH HOH 1061 A HOH 1062 3 HOH HOH 1062 A HOH 1063 3 HOH HOH 1063 A HOH 1064 3 HOH HOH 1064 A HOH 1065 3 HOH HOH 1065 A HOH 1066 3 HOH HOH 1066 A HOH 1067 3 HOH HOH 1067 A HOH 1068 3 HOH HOH 1068 A HOH 1069 3 HOH HOH 1069 A HOH 2002 3 HOH HOH 2002 A HOH 2003 3 HOH HOH 2003 A HOH 2004 3 HOH HOH 2004 A HOH 2005 3 HOH HOH 2005 A HOH 2006 3 HOH HOH 2006 A HOH 2007 3 HOH HOH 2007 A HOH 2008 3 HOH HOH 2008 A HOH 2009 3 HOH HOH 2009 A HOH 2010 3 HOH HOH 2010 A HOH 2011 3 HOH HOH 2011 A HOH 2012 3 HOH HOH 2012 A HOH 2013 3 HOH HOH 2013 A HOH 2014 3 HOH HOH 2014 A HOH 2015 3 HOH HOH 2015 A HOH 2016 3 HOH HOH 2016 A HOH 2017 3 HOH HOH 2017 A HOH 2018 3 HOH HOH 2018 A HOH 2019 3 HOH HOH 2019 A HOH 2020 3 HOH HOH 2020 A HOH 2021 3 HOH HOH 2021 A HOH 2022 3 HOH HOH 2022 A HOH 2023 3 HOH HOH 2023 A HOH 2024 3 HOH HOH 2024 A HOH 2025 3 HOH HOH 2025 A HOH 2026 3 HOH HOH 2026 A HOH 2027 3 HOH HOH 2027 A HOH 2028 3 HOH HOH 2028 A HOH 2029 3 HOH HOH 2029 A HOH 2030 3 HOH HOH 2030 A HOH 2032 3 HOH HOH 2032 A HOH 2033 3 HOH HOH 2033 A HOH 2034 3 HOH HOH 2034 A HOH 2035 3 HOH HOH 2035 A HOH 2036 3 HOH HOH 2036 A HOH 2037 3 HOH HOH 2037 A HOH 2041 3 HOH HOH 2041 A HOH 2043 3 HOH HOH 2043 A HOH 2045 3 HOH HOH 2045 A HOH 2046 3 HOH HOH 2046 A HOH 2047 3 HOH HOH 2047 A HOH 2049 3 HOH HOH 2049 A HOH 3001 3 HOH HOH 3001 A HOH 3002 3 HOH HOH 3002 A HOH 3003 3 HOH HOH 3003 A HOH 3004 3 HOH HOH 3004 A HOH 3005 3 HOH HOH 3005 A HOH 3006 3 HOH HOH 3006 A HOH 3007 3 HOH HOH 3007 A HOH 3008 3 HOH HOH 3008 A HOH 3009 3 HOH HOH 3009 A HOH 3011 3 HOH HOH 3011 A HOH 3012 3 HOH HOH 3012 A HOH 3014 3 HOH HOH 3014 A HOH 3015 3 HOH HOH 3015 A HOH 3016 3 HOH HOH 3016 A HOH 3017 3 HOH HOH 3017 A HOH 3018 3 HOH HOH 3018 A HOH 3019 3 HOH HOH 3019 A HOH 3020 3 HOH HOH 3020 A HOH 3021 3 HOH HOH 3021 A HOH 3022 3 HOH HOH 3022 A HOH 3026 3 HOH HOH 3026 A HOH 3028 3 HOH HOH 3028 A HOH 3029 3 HOH HOH 3029 A HOH 3031 3 HOH HOH 3031 A HOH 3032 3 HOH HOH 3032 A HOH 3033 3 HOH HOH 3033 A HOH 3034 3 HOH HOH 3034 A HOH 3035 3 HOH HOH 3035 A HOH 3039 3 HOH HOH 3039 A HOH 3040 3 HOH HOH 3040 A HOH 3041 3 HOH HOH 3041 A HOH 3044 3 HOH HOH 3044 A MET 1 n 1 MET 1 A GLU 2 n 2 GLU 2 A HIS 3 n 3 HIS 3 A VAL 4 n 4 VAL 4 A ALA 5 n 5 ALA 5 A PHE 6 n 6 PHE 6 A GLY 7 n 7 GLY 7 A SER 8 n 8 SER 8 A GLU 9 n 9 GLU 9 A ASP 10 n 10 ASP 10 A ILE 11 n 11 ILE 11 A GLU 12 n 12 GLU 12 A ASN 13 n 13 ASN 13 A THR 14 n 14 THR 14 A LEU 15 n 15 LEU 15 A ALA 16 n 16 ALA 16 A LYS 17 n 17 LYS 17 A MET 18 n 18 MET 18 A ASP 19 n 19 ASP 19 A ASP 20 n 20 ASP 20 A GLY 21 n 21 GLY 21 A GLN 22 n 22 GLN 22 A LEU 23 n 23 LEU 23 A ASP 24 n 24 ASP 24 A GLY 25 n 25 GLY 25 A LEU 26 n 26 LEU 26 A ALA 27 n 27 ALA 27 A PHE 28 n 28 PHE 28 A GLY 29 n 29 GLY 29 A ALA 30 n 30 ALA 30 A ILE 31 n 31 ILE 31 A GLN 32 n 32 GLN 32 A LEU 33 n 33 LEU 33 A ASP 34 n 34 ASP 34 A GLY 35 n 35 GLY 35 A ASP 36 n 36 ASP 36 A GLY 37 n 37 GLY 37 A ASN 38 n 38 ASN 38 A ILE 39 n 39 ILE 39 A LEU 40 n 40 LEU 40 A GLN 41 n 41 GLN 41 A TYR 42 n 42 TYR 42 A ASN 43 n 43 ASN 43 A ALA 44 n 44 ALA 44 A ALA 45 n 45 ALA 45 A GLU 46 n 46 GLU 46 A GLY 47 n 47 GLY 47 A ASP 48 n 48 ASP 48 A ILE 49 n 49 ILE 49 A THR 50 n 50 THR 50 A GLY 51 n 51 GLY 51 A ARG 52 n 52 ARG 52 A ASP 53 n 53 ASP 53 A PRO 54 n 54 PRO 54 A LYS 55 n 55 LYS 55 A GLN 56 n 56 GLN 56 A VAL 57 n 57 VAL 57 A ILE 58 n 58 ILE 58 A GLY 59 n 59 GLY 59 A LYS 60 n 60 LYS 60 A ASN 61 n 61 ASN 61 A PHE 62 n 62 PHE 62 A PHE 63 n 63 PHE 63 A LYS 64 n 64 LYS 64 A ASP 65 n 65 ASP 65 A VAL 66 n 66 VAL 66 A ALA 67 n 67 ALA 67 A PRO 68 n 68 PRO 68 A CYS 69 n 69 CYS 69 A THR 70 n 70 THR 70 A ASP 71 n 71 ASP 71 A SER 72 n 72 SER 72 A PRO 73 n 73 PRO 73 A GLU 74 n 74 GLU 74 A PHE 75 n 75 PHE 75 A TYR 76 n 76 TYR 76 A GLY 77 n 77 GLY 77 A LYS 78 n 78 LYS 78 A PHE 79 n 79 PHE 79 A LYS 80 n 80 LYS 80 A GLU 81 n 81 GLU 81 A GLY 82 n 82 GLY 82 A VAL 83 n 83 VAL 83 A ALA 84 n 84 ALA 84 A SER 85 n 85 SER 85 A GLY 86 n 86 GLY 86 A ASN 87 n 87 ASN 87 A LEU 88 n 88 LEU 88 A ASN 89 n 89 ASN 89 A THR 90 n 90 THR 90 A MET 91 n 91 MET 91 A PHE 92 n 92 PHE 92 A GLU 93 n 93 GLU 93 A TYR 94 n 94 TYR 94 A THR 95 n 95 THR 95 A PHE 96 n 96 PHE 96 A ASP 97 n 97 ASP 97 A TYR 98 n 98 TYR 98 A GLN 99 n 99 GLN 99 A MET 100 n 100 MET 100 A THR 101 n 101 THR 101 A PRO 102 n 102 PRO 102 A THR 103 n 103 THR 103 A LYS 104 n 104 LYS 104 A VAL 105 n 105 VAL 105 A LYS 106 n 106 LYS 106 A VAL 107 n 107 VAL 107 A HIS 108 n 108 HIS 108 A MET 109 n 109 MET 109 A LYS 110 n 110 LYS 110 A LYS 111 n 111 LYS 111 A ALA 112 n 112 ALA 112 A LEU 113 n 113 LEU 113 A SER 114 n 114 SER 114 A GLY 115 n 115 GLY 115 A ASP 116 n 116 ASP 116 A SER 117 n 117 SER 117 A TYR 118 n 118 TYR 118 A TRP 119 n 119 TRP 119 A VAL 120 n 120 VAL 120 A PHE 121 n 121 PHE 121 A VAL 122 n 122 VAL 122 A LYS 123 n 123 LYS 123 A ARG 124 n 124 ARG 124 A VAL 125 n 125 VAL 125 A 0.1213000 0.1326000 0.1428000 0.1548000 3511 4249 5 5 66807 author_defined_assembly 1 monomeric 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 THR 90 A O THR 90 A N MET 109 A N MET 109 A O LYS 106 A O LYS 106 A N LYS 123 A N LYS 123 A O TYR 118 A O TYR 118 A N LEU 33 A N LEU 33 A O GLN 32 A O GLN 32 A N GLN 41 A N GLN 41 1 A HOH 2004 C HOH 1 A HOH 3001 C HOH 1 A HOH 3002 C HOH 1 A A H HE22 ASP GLN 19 22 1.19 1 A A HZ3 O LYS HOH 78 3003 1.47 1 A A OD1 OE1 ASP GLN 20 41 2.02 A 1 A A NZ O LYS HOH 78 3003 2.09 1 A A OD2 O ASP HOH 20 3044 2.11 1 A A O O HOH HOH 1068 1069 2.14 1 13.44 2.20 113.40 126.84 A A A CA CB CG ASP ASP ASP 65 65 65 N 1 -11.10 0.90 118.30 107.20 A A A CB CG OD1 ASP ASP ASP 65 65 65 N 1 12.91 0.90 118.30 131.21 A A A CB CG OD2 ASP ASP ASP 65 65 65 N 1 12.79 1.10 114.20 126.99 A A A CA CB SG CYS CYS CYS 69 69 69 B B B N 1 -4.74 0.60 121.00 116.26 A A A CB CG CD2 TYR TYR TYR 76 76 76 N 1 3.61 0.60 121.00 124.61 A A A CB CG CD1 TYR TYR TYR 76 76 76 N 1 -8.84 1.20 123.30 114.46 A A A OE1 CD OE2 GLU GLU GLU 81 81 81 N 1 13.45 2.00 118.30 131.75 A A A CG CD OE1 GLU GLU GLU 81 81 81 N 1 6.10 0.90 118.30 124.40 A A A CB CG OD2 ASP ASP ASP 97 97 97 B B B N 1 -4.86 0.60 121.00 116.14 A A A CB CG CD2 TYR TYR TYR 98 98 98 A A A N 1 3.70 0.60 121.00 124.70 A A A CB CG CD2 TYR TYR TYR 98 98 98 B B B N 1 -14.84 1.60 100.20 85.36 A A A CG SD CE MET MET MET 109 109 109 N 1 6.74 0.90 118.30 125.04 A A A CB CG OD2 ASP ASP ASP 116 116 116 N 1 -4.73 0.50 120.30 115.57 A A A NE CZ NH2 ARG ARG ARG 124 124 124 N 1 A HIS 3 -101.78 77.25 1 A PHE 75 -131.44 -75.53 1 A ASN 89 -160.31 97.87 1 A ASP 97 A -140.97 11.16 1 A ASP 97 B -150.35 24.03 NUMBER OF PROTEIN AND SOLVENT ATOMS CONTAINS DUAL CONFORMERS 0.1548000 0.1326000 0.85 50 11379 4249 80680 15920 5 97.7 5% RANDOMLY CHOSEN BY SHELX 1 FREE R-VALUE 0 SAME CRYSTAL LATTICE MOLECULAR REPLACEMENT 2PHY ENGH AND HUBER MOEWS & KRETSINGER 18 943 1133 0.85 50 196 1301 11 0 1094 0.017 0.038 0.098 0.112 0.064 0.85 3PYP 84934 0 0.0420000 0.0420000 1 10.9 6.6 97.7 0.5200000 0.85 0.86 1.7 0.5200000 87.1 refinement SHELX-97 data reduction DENZO data scaling SCALEPACK PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE 1 N N 2 N N 3 N N A ILE 11 A ILE 11 HELX_P A THR 14 A THR 14 1 1 4 A ASP 20 A ASP 20 HELX_P A GLY 25 A GLY 25 1 2 6 A ALA 44 A ALA 44 HELX_P A THR 50 A THR 50 1 3 7 A PRO 54 A PRO 54 HELX_P A VAL 57 A VAL 57 1 4 4 A PRO 68 A PRO 68 HELX_P A THR 70 A THR 70 5 5 3 A TYR 76 A TYR 76 HELX_P A SER 85 A SER 85 1 6 10 covale 1.840 one A A A CYS 69 A SG CYS 69 1_555 A HC4 126 B C1 HC4 1_555 covale 1.793 one B B A CYS 69 A SG CYS 69 1_555 A HC4 126 B C1 HC4 1_555 PHOTORECEPTOR PHOTORECEPTOR, LIGHT SENSOR FOR NEGATIVE PHOTOTAXIS PYP_ECTHA UNP 1 1 P16113 MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV 1 125 3PYP 1 125 P16113 A 1 1 125 5 anti-parallel anti-parallel anti-parallel anti-parallel A ASN 89 A ASN 89 A PHE 96 A PHE 96 A THR 103 A THR 103 A LYS 111 A LYS 111 A TYR 118 A TYR 118 A ARG 124 A ARG 124 A GLY 29 A GLY 29 A LEU 33 A LEU 33 A ILE 39 A ILE 39 A TYR 42 A TYR 42 BINDING SITE FOR RESIDUE HC4 A 126 A HC4 126 Software 13 A ILE 31 A ILE 31 13 1_555 A TYR 42 A TYR 42 13 1_555 A GLU 46 A GLU 46 13 1_555 A THR 50 A THR 50 13 1_555 A ARG 52 A ARG 52 13 1_555 A PHE 62 A PHE 62 13 1_555 A VAL 66 A VAL 66 13 1_555 A ALA 67 A ALA 67 13 1_555 A PRO 68 A PRO 68 13 1_555 A CYS 69 A CYS 69 13 1_555 A THR 70 A THR 70 13 1_555 A PHE 96 A PHE 96 13 1_555 A TYR 98 A TYR 98 13 1_555 173 P 63