0.014944 0.008628 0.000000 0.000000 0.017256 0.000000 0.000000 0.000000 0.024389 0.000000 0.000000 0.000000 Rajagopal, S. Anderson, S. Srajer, V. Schmidt, M. Pahl, R. Moffat, K. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 66.917 66.917 41.002 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 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 Structure STRUE6 2005 0969-2126 13 55 63 10.1016/j.str.2004.10.016 15642261 A Structural Pathway for Signaling in the E46Q Mutant of Photoactive Yellow Protein 2005 10.2210/pdb1t1c/pdb pdb_00001t1c 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 288 1 CCD MARRESEARCH LAUE L x-ray 1 1.0 14-ID-B APS SYNCHROTRON APS BEAMLINE 14-ID-B 13887.591 Photoactive yellow protein E46Q 1 man polymer 164.158 4'-HYDROXYCINNAMIC ACID 1 syn non-polymer PYP no no MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAQGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAQGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK 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 Escherichia sample PYP 1053 Halorhodospira halophila 562 Escherichia coli 1.91 35.54 VAPOR DIFFUSION, HANGING DROP 7 ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 software database_2 struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Other Refinement description Database references Derived calculations 1 0 2005-01-18 1 1 2008-04-30 1 2 2011-07-13 1 3 2015-09-09 1 4 2017-10-11 1 5 2021-10-27 _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2004-04-15 REL REL HC4 4'-HYDROXYCINNAMIC ACID CYS 69 2 HC4 HC4 169 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 GLN 46 n 46 GLN 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 0.1294 0.1294 12593 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 LEU 40 A O LEU 40 A N GLN 32 A N GLN 32 A N LEU 33 A N LEU 33 A O TYR 118 A O TYR 118 A O PHE 121 A O PHE 121 A N HIS 108 A N HIS 108 A O VAL 107 A O VAL 107 A N PHE 92 A N PHE 92 1 -4.32 0.50 120.30 115.98 A A A NE CZ NH1 ARG ARG ARG 52 52 52 N 1 5.26 0.70 120.80 126.06 A A A CB CG CD1 PHE PHE PHE 75 75 75 N 1 4.70 0.60 121.00 125.70 A A A CB CG CD1 TYR TYR TYR 76 76 76 N 1 4.68 0.60 121.00 125.68 A A A CB CG CD2 TYR TYR TYR 94 94 94 N 2 -6.99 0.90 118.30 111.31 A A A CB CG OD1 ASP ASP ASP 65 65 65 N 2 6.42 0.90 118.30 124.72 A A A CB CG OD2 ASP ASP ASP 65 65 65 N 2 -3.71 0.60 121.00 117.29 A A A CB CG CD2 TYR TYR TYR 76 76 76 N 2 3.85 0.60 121.00 124.85 A A A CB CG CD2 TYR TYR TYR 94 94 94 N 2 -3.72 0.60 121.00 117.28 A A A CB CG CD1 TYR TYR TYR 94 94 94 N 2 -10.26 1.60 100.20 89.94 A A A CG SD CE MET MET MET 109 109 109 N 2 15.11 2.50 113.10 128.21 A A A N CA C GLY GLY GLY 115 115 115 N 2 5.23 0.50 120.30 125.53 A A A NE CZ NH1 ARG ARG ARG 124 124 124 N 2 -8.07 0.50 120.30 112.23 A A A NE CZ NH2 ARG ARG ARG 124 124 124 N 1 A A CB SG CYS CYS 69 69 0.131 0.017 1.818 1.949 N 1 A PHE 75 -126.63 -72.10 1 A ASN 89 -162.12 95.62 1 A ASP 116 -105.40 55.91 2 A PHE 75 -130.94 -76.15 2 A ASN 89 -160.49 97.44 2 A ASP 97 -143.89 17.21 2 A ASP 116 -119.63 58.70 0.1386 0.1285 0.1294 0.1294 1.60 30.00 3951 1310 13947 13947 10993 100 RANDOM 1 FREE R 0.0 AB INITIO ENGH AND HUBER 125 0.00 987.00 1.60 30.00 0 987 11 0 976 0.013 0.030 0.000 0.0263 0.071 0.083 0.027 0.000 0.058 0.000 1.6 30 1T1C 13957 1 model building SHELX refinement SHELXL-97 data scaling LaueView Late intermediate IL3 from time-resolved crystallography of the E46Q mutant of PYP 1 N N 2 N N A ASP 10 A ASP 10 HELX_P A LYS 17 A LYS 17 1 1 8 A ASP 19 A ASP 19 HELX_P A ASP 24 A ASP 24 1 2 6 A ASN 43 A ASN 43 HELX_P A GLY 51 A GLY 51 1 3 9 A ASP 53 A ASP 53 HELX_P A ILE 58 A ILE 58 1 4 6 A ALA 67 A ALA 67 HELX_P A ASP 71 A ASP 71 5 5 5 A PHE 75 A PHE 75 HELX_P A GLY 86 A GLY 86 1 6 12 covale 1.752 one A CYS 69 A SG CYS 69 1_555 A HC4 169 B C1 HC4 1_555 photoreceptor photoactive yellow protein, PAS domain, photoreceptor PYP_ECTHA UNP 1 1 P16113 MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV 1 125 1T1C 1 125 P16113 A 1 1 125 1 GLU engineered mutation GLN 46 1T1C A P16113 UNP 46 46 5 anti-parallel anti-parallel anti-parallel anti-parallel A ILE 39 A ILE 39 A TYR 42 A TYR 42 A GLY 29 A GLY 29 A ASP 34 A ASP 34 A SER 117 A SER 117 A ARG 124 A ARG 124 A THR 103 A THR 103 A LYS 111 A LYS 111 A ASN 89 A ASN 89 A PHE 96 A PHE 96 BINDING SITE FOR RESIDUE HC4 A 169 A HC4 169 Software 9 A TYR 42 A TYR 42 9 1_555 A GLN 46 A GLN 46 9 1_555 A THR 50 A THR 50 9 1_555 A ARG 52 A ARG 52 9 1_555 A ALA 67 A ALA 67 9 1_555 A PRO 68 A PRO 68 9 1_555 A CYS 69 A CYS 69 9 1_555 A PHE 96 A PHE 96 9 1_555 A TYR 98 A TYR 98 9 1_555 173 P 63