0.028596 0.000000 0.000000 0.000000 0.016358 0.000000 0.000000 0.000000 0.014206 0.00000 0.00000 0.00000 Zhang, X.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 34.970 61.134 70.391 C2 H4 O2 60.052 ACETIC ACID non-polymer 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 Cd 2 112.411 CADMIUM ION non-polymer 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 C4 H9 N O3 119.119 y THREONINE 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 Biochem.Biophys.Res.Commun. BBRCA9 0146 1090-2104 450 929 935 10.1016/j.bbrc.2014.06.053 24952155 Atomic resolution structure of the E. coli YajR transporter YAM domain. 2014 10.2210/pdb4q2l/pdb pdb_00004q2l 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2012-10-23 ADSC QUANTUM 270 SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH M x-ray 1 0.9500 1.0 BL-17A Photon Factory 0.9500 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 7858.906 Major facilitator superfamily MFS_1 YAM domain, UNP residues 388-454 1 man polymer 60.052 ACETIC ACID 2 syn non-polymer 112.411 CADMIUM ION 2 syn non-polymer 18.015 water 89 nat water Predicted transporter, YajR MFS transporter no no GSHMKEPPYVSSLRIEIPADIAANEALKVRLLETEGVKEVLIAEEEHSAYVKIDSKVTNRFEVEQAIRQA GSHMKEPPYVSSLRIEIPADIAANEALKVRLLETEGVKEVLIAEEEHSAYVKIDSKVTNRFEVEQAIRQA 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 B / BL21-DE3 sample B21_00379, E. coli, ECBD_3234, ECD_00375, yajR 469008 Escherichia coli 562 Escherichia coli BL21 pET-28a 1 2.39 48.61 VAPOR DIFFUSION, HANGING DROP 7.5 0.1M HEPES (pH 7.5), 50mM CdSO4, 1.0M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 289K 289 citation database_2 pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Database references Derived calculations 1 0 2014-07-09 1 1 2022-08-24 _citation.journal_volume _citation.page_first _citation.page_last _citation.title _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id _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_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Similar protein folding. RCSB Y PDBJ 2014-04-09 REL REL ACY ACETIC ACID CD CADMIUM ION HOH water ACY 3004 2 ACY ACY 101 A ACY 3005 2 ACY ACY 102 A CD 2001 3 CD CD 103 A CD 2002 3 CD CD 104 A HOH 1001 4 HOH HOH 1001 A HOH 1002 4 HOH HOH 1002 A HOH 1003 4 HOH HOH 1003 A HOH 1004 4 HOH HOH 1004 A HOH 1005 4 HOH HOH 1005 A HOH 1006 4 HOH HOH 1006 A HOH 1007 4 HOH HOH 1007 A HOH 1008 4 HOH HOH 1008 A HOH 1009 4 HOH HOH 1009 A HOH 1010 4 HOH HOH 1010 A HOH 1011 4 HOH HOH 1011 A HOH 1012 4 HOH HOH 1012 A HOH 1013 4 HOH HOH 1013 A HOH 1014 4 HOH HOH 1014 A HOH 1015 4 HOH HOH 1015 A HOH 1016 4 HOH HOH 1016 A HOH 1017 4 HOH HOH 1017 A HOH 1018 4 HOH HOH 1018 A HOH 1019 4 HOH HOH 1019 A HOH 1020 4 HOH HOH 1020 A HOH 1021 4 HOH HOH 1021 A HOH 1022 4 HOH HOH 1022 A HOH 1023 4 HOH HOH 1023 A HOH 1024 4 HOH HOH 1024 A HOH 1025 4 HOH HOH 1025 A HOH 1026 4 HOH HOH 1026 A HOH 1027 4 HOH HOH 1027 A HOH 1028 4 HOH HOH 1028 A HOH 1029 4 HOH HOH 1029 A HOH 1030 4 HOH HOH 1030 A HOH 1031 4 HOH HOH 1031 A HOH 1032 4 HOH HOH 1032 A HOH 1033 4 HOH HOH 1033 A HOH 1034 4 HOH HOH 1034 A HOH 1035 4 HOH HOH 1035 A HOH 1036 4 HOH HOH 1036 A HOH 1037 4 HOH HOH 1037 A HOH 1038 4 HOH HOH 1038 A HOH 1039 4 HOH HOH 1039 A HOH 1040 4 HOH HOH 1040 A HOH 1041 4 HOH HOH 1041 A HOH 1042 4 HOH HOH 1042 A HOH 1043 4 HOH HOH 1043 A HOH 1044 4 HOH HOH 1044 A HOH 1045 4 HOH HOH 1045 A HOH 1046 4 HOH HOH 1046 A HOH 1047 4 HOH HOH 1047 A HOH 1048 4 HOH HOH 1048 A HOH 1049 4 HOH HOH 1049 A HOH 1050 4 HOH HOH 1050 A HOH 1051 4 HOH HOH 1051 A HOH 1052 4 HOH HOH 1052 A HOH 1053 4 HOH HOH 1053 A HOH 1054 4 HOH HOH 1054 A HOH 1055 4 HOH HOH 1055 A HOH 1056 4 HOH HOH 1056 A HOH 1057 4 HOH HOH 1057 A HOH 1058 4 HOH HOH 1058 A HOH 1059 4 HOH HOH 1059 A HOH 1060 4 HOH HOH 1060 A HOH 1061 4 HOH HOH 1061 A HOH 1062 4 HOH HOH 1062 A HOH 1063 4 HOH HOH 1063 A HOH 1064 4 HOH HOH 1064 A HOH 1065 4 HOH HOH 1065 A HOH 1066 4 HOH HOH 1066 A HOH 1067 4 HOH HOH 1067 A HOH 1068 4 HOH HOH 1068 A HOH 1069 4 HOH HOH 1069 A HOH 1070 4 HOH HOH 1070 A HOH 1071 4 HOH HOH 1071 A HOH 1072 4 HOH HOH 1072 A HOH 1073 4 HOH HOH 1073 A HOH 1074 4 HOH HOH 1074 A HOH 1075 4 HOH HOH 1075 A HOH 1076 4 HOH HOH 1076 A HOH 1077 4 HOH HOH 1077 A HOH 1078 4 HOH HOH 1078 A HOH 1079 4 HOH HOH 1079 A HOH 1080 4 HOH HOH 1080 A HOH 1081 4 HOH HOH 1081 A HOH 1082 4 HOH HOH 1082 A HOH 1083 4 HOH HOH 1083 A HOH 1084 4 HOH HOH 1084 A HOH 1085 4 HOH HOH 1085 A HOH 1086 4 HOH HOH 1086 A HOH 1087 4 HOH HOH 1087 A HOH 1088 4 HOH HOH 1088 A HOH 1089 4 HOH HOH 1089 A n 1 -2 A n 2 -1 A n 3 0 A n 4 1 A n 5 2 A n 6 3 A PRO 4 n 7 PRO 4 A PRO 5 n 8 PRO 5 A TYR 6 n 9 TYR 6 A VAL 7 n 10 VAL 7 A SER 8 n 11 SER 8 A SER 9 n 12 SER 9 A LEU 10 n 13 LEU 10 A ARG 11 n 14 ARG 11 A ILE 12 n 15 ILE 12 A GLU 13 n 16 GLU 13 A ILE 14 n 17 ILE 14 A PRO 15 n 18 PRO 15 A ALA 16 n 19 ALA 16 A ASP 17 n 20 ASP 17 A ILE 18 n 21 ILE 18 A ALA 19 n 22 ALA 19 A ALA 20 n 23 ALA 20 A ASN 21 n 24 ASN 21 A GLU 22 n 25 GLU 22 A ALA 23 n 26 ALA 23 A LEU 24 n 27 LEU 24 A LYS 25 n 28 LYS 25 A VAL 26 n 29 VAL 26 A ARG 27 n 30 ARG 27 A LEU 28 n 31 LEU 28 A LEU 29 n 32 LEU 29 A GLU 30 n 33 GLU 30 A THR 31 n 34 THR 31 A GLU 32 n 35 GLU 32 A GLY 33 n 36 GLY 33 A VAL 34 n 37 VAL 34 A LYS 35 n 38 LYS 35 A GLU 36 n 39 GLU 36 A VAL 37 n 40 VAL 37 A LEU 38 n 41 LEU 38 A ILE 39 n 42 ILE 39 A ALA 40 n 43 ALA 40 A GLU 41 n 44 GLU 41 A GLU 42 n 45 GLU 42 A GLU 43 n 46 GLU 43 A HIS 44 n 47 HIS 44 A SER 45 n 48 SER 45 A ALA 46 n 49 ALA 46 A TYR 47 n 50 TYR 47 A VAL 48 n 51 VAL 48 A LYS 49 n 52 LYS 49 A ILE 50 n 53 ILE 50 A ASP 51 n 54 ASP 51 A SER 52 n 55 SER 52 A LYS 53 n 56 LYS 53 A VAL 54 n 57 VAL 54 A THR 55 n 58 THR 55 A ASN 56 n 59 ASN 56 A ARG 57 n 60 ARG 57 A PHE 58 n 61 PHE 58 A GLU 59 n 62 GLU 59 A VAL 60 n 63 VAL 60 A GLU 61 n 64 GLU 61 A GLN 62 n 65 GLN 62 A ALA 63 n 66 ALA 63 A ILE 64 n 67 ILE 64 A ARG 65 n 68 ARG 65 A GLN 66 n 69 GLN 66 A ALA 67 n 70 ALA 67 A author_and_software_defined_assembly PISA 2 dimeric 1210 -29 7810 A GLU 13 A A OE2 GLU 16 1_555 A CD 104 E CD CD 1_555 A GLU 43 A O GLU 46 1_555 89.2 A GLU 13 A A OE2 GLU 16 1_555 A CD 104 E CD CD 1_555 A HOH 1035 F O HOH 1_555 86.1 A GLU 43 A O GLU 46 1_555 A CD 104 E CD CD 1_555 A HOH 1035 F O HOH 1_555 89.3 A GLU 13 A A OE2 GLU 16 1_555 A CD 104 E CD CD 1_555 A HOH 1088 F O HOH 1_555 80.3 A GLU 43 A O GLU 46 1_555 A CD 104 E CD CD 1_555 A HOH 1088 F O HOH 1_555 165.7 A HOH 1035 F O HOH 1_555 A CD 104 E CD CD 1_555 A HOH 1088 F O HOH 1_555 99.6 A HIS 44 A ND1 HIS 47 1_555 A CD 103 D CD CD 1_555 A ACY 101 B O ACY 1_555 141.5 A HIS 44 A ND1 HIS 47 1_555 A CD 103 D CD CD 1_555 A HOH 1039 F O HOH 1_555 95.7 A ACY 101 B O ACY 1_555 A CD 103 D CD CD 1_555 A HOH 1039 F O HOH 1_555 83.8 A HIS 44 A ND1 HIS 47 1_555 A CD 103 D CD CD 1_555 A HOH 1040 F O HOH 1_555 89.2 A ACY 101 B O ACY 1_555 A CD 103 D CD CD 1_555 A HOH 1040 F O HOH 1_555 88.4 A HOH 1039 F O HOH 1_555 A CD 103 D CD CD 1_555 A HOH 1040 F O HOH 1_555 172.0 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 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 4_575 x,-y+2,-z crystal symmetry operation 0.0000000000 122.2680000000 0.0000000000 A N ILE 12 A N ILE 15 A O ALA 46 A O ALA 49 A O LYS 49 A O LYS 52 A N LYS 35 A N LYS 38 1 A HOH 1037 F HOH 1 A HOH 1045 F HOH 1 A HOH 1078 F HOH 1 A GLY -2 A GLY 1 1 Y 1 A SER -1 A SER 2 1 Y 1 A HIS 0 A HIS 3 1 Y 1 A MET 1 A MET 4 1 Y 1 A LYS 2 A LYS 5 1 Y 1 A GLU 3 A GLU 6 1 Y 1 A A O O HOH HOH 1058 1083 2.08 1 A A OE1 O GLU HOH 61 1081 2.08 A 1 A A O OG TYR SER 6 52 2.10 1 A A NZ O LYS HOH 35 1084 2.12 1 A A NZ O LYS HOH 25 1042 2.19 B 1 12.86 2.10 128.40 141.26 A A A C N CD PRO PRO PRO 4 5 5 Y 1 A A OE2 O GLU HOH 42 1082 2.14 B 1_555 4_575 0.1986 0.1831 0.1839 1.071 28.038 1676 32553 31032 5.12 97.45 0.07 1 0.81 SAD 17.61 1.10 1.30 MLHL FLAT BULK SOLVENT MODEL 1.071 28.038 89 605 10 0 506 0.007 584 1.242 803 16.151 244 0.086 95 0.005 108 0.2894 0.2743 1.1028 138 2480 12 95.00 0.2425 0.2050 1.1384 136 2498 12 96.00 0.2203 0.1711 1.1791 138 2502 12 96.00 0.1852 0.1666 1.2263 131 2542 12 97.00 0.2193 0.1881 1.2821 141 2540 12 97.00 0.1663 0.1558 1.3497 142 2583 12 97.00 0.1800 0.1532 1.4342 134 2576 12 99.00 0.1693 0.1519 1.5450 139 2614 12 98.00 0.1728 0.1516 1.7004 146 2600 12 99.00 0.1823 0.1707 1.9464 148 2652 12 99.00 0.1550 0.1856 2.4521 147 2677 12 100.00 0.2434 0.2023 28.0472 136 2763 12 98.00 1.07 50.0 4Q2L 32553 31739 3.0 3.0 0.051 1 31.7 7.3 97.5 0.889 1.07 1.11 3.0 3147 1 7.1 95.3 data collection ADSC Quantum phasing PHASES refinement PHENIX (phenix.refine: 1.8_1069) data reduction HKL-2000 data scaling HKL-2000 Atomic Resolution Structure of the E. coli YajR Transporter YAM Domain 1 N N 2 N N 2 N N 3 N N 3 N N 4 N N A ASN 21 A ASN 24 HELX_P A GLU 30 A GLU 33 1 1 10 A ASN 56 A ASN 59 HELX_P A GLN 66 A GLN 69 1 2 11 metalc 2.539 A A GLU 13 A OE2 GLU 16 1_555 A CD 104 E CD CD 1_555 metalc 2.268 A GLU 43 A O GLU 46 1_555 A CD 104 E CD CD 1_555 metalc 2.312 A HIS 44 A ND1 HIS 47 1_555 A CD 103 D CD CD 1_555 metalc 2.628 A ACY 101 B O ACY 1_555 A CD 103 D CD CD 1_555 metalc 2.352 A CD 103 D CD CD 1_555 A HOH 1039 F O HOH 1_555 metalc 2.467 A CD 103 D CD CD 1_555 A HOH 1040 F O HOH 1_555 metalc 2.634 A CD 104 E CD CD 1_555 A HOH 1035 F O HOH 1_555 metalc 2.602 A CD 104 E CD CD 1_555 A HOH 1088 F O HOH 1_555 TRANSPORT PROTEIN Feredoxin Fold, transporter, TRANSPORT PROTEIN C6EL42_ECOBD UNP 1 388 C6EL42 MKEPPYVSSLRIEIPADIAANEALKVRLLETEGVKEVLIAEEEHSAYVKIDSKVTNRFEVEQAIRQA 388 454 4Q2L 1 67 C6EL42 A 1 4 70 1 expression tag GLY -2 4Q2L A C6EL42 UNP 1 1 expression tag SER -1 4Q2L A C6EL42 UNP 2 1 expression tag HIS 0 4Q2L A C6EL42 UNP 3 3 anti-parallel anti-parallel A VAL 7 A VAL 10 A GLU 13 A GLU 16 A SER 45 A SER 48 A ASP 51 A ASP 54 A VAL 34 A VAL 37 A ALA 40 A ALA 43 BINDING SITE FOR RESIDUE ACY A 101 A ACY 101 Software 7 BINDING SITE FOR RESIDUE ACY A 102 A ACY 102 Software 4 BINDING SITE FOR RESIDUE CD A 103 A CD 103 Software 5 BINDING SITE FOR RESIDUE CD A 104 A CD 104 Software 5 A GLU 30 A GLU 33 7 8_475 A GLU 41 A GLU 44 7 1_555 A GLU 42 A GLU 45 7 1_555 A HIS 44 A HIS 47 7 1_555 A CD 103 D CD 7 1_555 A HOH 1051 F HOH 7 1_555 A HOH 1074 F HOH 7 1_555 A SER 52 A SER 55 4 1_555 A LYS 53 A LYS 56 4 3_655 A ASN 56 A ASN 59 4 1_555 A HOH 1065 F HOH 4 1_555 A GLU 30 A GLU 33 5 8_475 A HIS 44 A HIS 47 5 1_555 A ACY 101 B ACY 5 1_555 A HOH 1039 F HOH 5 1_555 A HOH 1040 F HOH 5 1_555 A GLU 13 A GLU 16 5 1_555 A GLU 42 A GLU 45 5 4_575 A GLU 43 A GLU 46 5 1_555 A HOH 1035 F HOH 5 1_555 A HOH 1088 F HOH 5 1_555 20 C 2 2 21