0.017986 0.000000 0.000000 0.000000 0.017986 0.000000 0.000000 0.000000 0.010438 0.00000 0.00000 0.00000 Stout, C.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 55.600 55.600 95.800 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 Fe3 S4 295.795 FE3-S4 CLUSTER 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 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 Fe4 S4 351.640 IRON/SULFUR CLUSTER 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 GW J.Biol.Inorg.Chem. JJBCFA 2154 0949-8257 3 140 149 -1 Crystal structures of ferricyanide-oxidized [Fe-S] clusters in Azotobacter vinelandii ferredoxin I. 1998 10.2210/pdb1axq/pdb pdb_00001axq 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 291 1 AREA DETECTOR 1996-01-10 SIEMENS GRAPHITE(002) M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RUH2R THIS 7FE FERREDOXIN FROM A. VINELANDII TREATED WITH 9\:1 MOLE RATIO OF FERRICYANIDE IN THE CRYSTALS. THE [FE-S] CLUSTERS HAVE BEEN PARTIALLY OXIDIZED. 12059.530 FERREDOXIN 1 man polymer 351.640 IRON/SULFUR CLUSTER 1 syn non-polymer 295.795 FE3-S4 CLUSTER 1 syn non-polymer no no AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPN ITEKKDPLPDAEDWDGVKGKLQHLER AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPN ITEKKDPLPDAEDWDGVKGKLQHLER 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 Azotobacter JG100 Azotobacter sample WILD TYPE FERREDOXIN OVER-EXPRESSED FROM A PLASMID IN A. VINELANDII FDXA 354 Azotobacter vinelandii FDXA 354 Azotobacter vinelandii JG100 PKT320 1 2.8 59.90 7.8 4.8 M AMMONIUM SULFATE, 0.45 M TRIS-HCL PH 7.8 database_2 pdbx_database_status pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Refinement description 1 0 1998-01-28 1 1 2008-03-24 1 2 2011-07-13 1 3 2023-08-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value _struct_conn.pdbx_dist_value _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 1997-10-17 REL SF4 IRON/SULFUR CLUSTER F3S FE3-S4 CLUSTER 5FD1 PDB ENTRY 5FD1 PDB experimental model FS4 107 2 SF4 SF4 107 A FS3 108 3 F3S F3S 108 A ALA 1 n 1 ALA 1 A PHE 2 n 2 PHE 2 A VAL 3 n 3 VAL 3 A VAL 4 n 4 VAL 4 A THR 5 n 5 THR 5 A ASP 6 n 6 ASP 6 A ASN 7 n 7 ASN 7 A CYS 8 n 8 CYS 8 A ILE 9 n 9 ILE 9 A LYS 10 n 10 LYS 10 A CYS 11 n 11 CYS 11 A LYS 12 n 12 LYS 12 A TYR 13 n 13 TYR 13 A THR 14 n 14 THR 14 A ASP 15 n 15 ASP 15 A CYS 16 n 16 CYS 16 A VAL 17 n 17 VAL 17 A GLU 18 n 18 GLU 18 A VAL 19 n 19 VAL 19 A CYS 20 n 20 CYS 20 A PRO 21 n 21 PRO 21 A VAL 22 n 22 VAL 22 A ASP 23 n 23 ASP 23 A CYS 24 n 24 CYS 24 A PHE 25 n 25 PHE 25 A TYR 26 n 26 TYR 26 A GLU 27 n 27 GLU 27 A GLY 28 n 28 GLY 28 A PRO 29 n 29 PRO 29 A ASN 30 n 30 ASN 30 A PHE 31 n 31 PHE 31 A LEU 32 n 32 LEU 32 A VAL 33 n 33 VAL 33 A ILE 34 n 34 ILE 34 A HIS 35 n 35 HIS 35 A PRO 36 n 36 PRO 36 A ASP 37 n 37 ASP 37 A GLU 38 n 38 GLU 38 A CYS 39 n 39 CYS 39 A ILE 40 n 40 ILE 40 A ASP 41 n 41 ASP 41 A CYS 42 n 42 CYS 42 A ALA 43 n 43 ALA 43 A LEU 44 n 44 LEU 44 A CYS 45 n 45 CYS 45 A GLU 46 n 46 GLU 46 A PRO 47 n 47 PRO 47 A GLU 48 n 48 GLU 48 A CYS 49 n 49 CYS 49 A PRO 50 n 50 PRO 50 A ALA 51 n 51 ALA 51 A GLN 52 n 52 GLN 52 A ALA 53 n 53 ALA 53 A ILE 54 n 54 ILE 54 A PHE 55 n 55 PHE 55 A SER 56 n 56 SER 56 A GLU 57 n 57 GLU 57 A ASP 58 n 58 ASP 58 A GLU 59 n 59 GLU 59 A VAL 60 n 60 VAL 60 A PRO 61 n 61 PRO 61 A GLU 62 n 62 GLU 62 A ASP 63 n 63 ASP 63 A MET 64 n 64 MET 64 A GLN 65 n 65 GLN 65 A GLU 66 n 66 GLU 66 A PHE 67 n 67 PHE 67 A ILE 68 n 68 ILE 68 A GLN 69 n 69 GLN 69 A LEU 70 n 70 LEU 70 A ASN 71 n 71 ASN 71 A ALA 72 n 72 ALA 72 A GLU 73 n 73 GLU 73 A LEU 74 n 74 LEU 74 A ALA 75 n 75 ALA 75 A GLU 76 n 76 GLU 76 A VAL 77 n 77 VAL 77 A TRP 78 n 78 TRP 78 A PRO 79 n 79 PRO 79 A ASN 80 n 80 ASN 80 A ILE 81 n 81 ILE 81 A THR 82 n 82 THR 82 A GLU 83 n 83 GLU 83 A LYS 84 n 84 LYS 84 A LYS 85 n 85 LYS 85 A ASP 86 n 86 ASP 86 A PRO 87 n 87 PRO 87 A LEU 88 n 88 LEU 88 A PRO 89 n 89 PRO 89 A ASP 90 n 90 ASP 90 A ALA 91 n 91 ALA 91 A GLU 92 n 92 GLU 92 A ASP 93 n 93 ASP 93 A TRP 94 n 94 TRP 94 A ASP 95 n 95 ASP 95 A GLY 96 n 96 GLY 96 A VAL 97 n 97 VAL 97 A LYS 98 n 98 LYS 98 A GLY 99 n 99 GLY 99 A LYS 100 n 100 LYS 100 A LEU 101 n 101 LEU 101 A GLN 102 n 102 GLN 102 A HIS 103 n 103 HIS 103 A LEU 104 n 104 LEU 104 A GLU 105 n 105 GLU 105 A ARG 106 n 106 ARG 106 A author_defined_assembly 1 monomeric A CYS 8 A SG CYS 8 1_555 A F3S 108 C FE3 F3S 1_555 A F3S 108 C S1 F3S 1_555 114.4 A CYS 8 A SG CYS 8 1_555 A F3S 108 C FE3 F3S 1_555 A F3S 108 C S3 F3S 1_555 119.2 A F3S 108 C S1 F3S 1_555 A F3S 108 C FE3 F3S 1_555 A F3S 108 C S3 F3S 1_555 98.4 A CYS 8 A SG CYS 8 1_555 A F3S 108 C FE3 F3S 1_555 A F3S 108 C S4 F3S 1_555 110.9 A F3S 108 C S1 F3S 1_555 A F3S 108 C FE3 F3S 1_555 A F3S 108 C S4 F3S 1_555 112.3 A F3S 108 C S3 F3S 1_555 A F3S 108 C FE3 F3S 1_555 A F3S 108 C S4 F3S 1_555 100.5 A CYS 16 A SG CYS 16 1_555 A F3S 108 C FE1 F3S 1_555 A F3S 108 C S1 F3S 1_555 119.3 A CYS 16 A SG CYS 16 1_555 A F3S 108 C FE1 F3S 1_555 A F3S 108 C S2 F3S 1_555 119.9 A F3S 108 C S1 F3S 1_555 A F3S 108 C FE1 F3S 1_555 A F3S 108 C S2 F3S 1_555 107.5 A CYS 16 A SG CYS 16 1_555 A F3S 108 C FE1 F3S 1_555 A F3S 108 C S3 F3S 1_555 115.8 A F3S 108 C S1 F3S 1_555 A F3S 108 C FE1 F3S 1_555 A F3S 108 C S3 F3S 1_555 91.5 A F3S 108 C S2 F3S 1_555 A F3S 108 C FE1 F3S 1_555 A F3S 108 C S3 F3S 1_555 97.3 A CYS 20 A SG CYS 20 1_555 A SF4 107 B FE4 SF4 1_555 A SF4 107 B S1 SF4 1_555 104.2 A CYS 20 A SG CYS 20 1_555 A SF4 107 B FE4 SF4 1_555 A SF4 107 B S2 SF4 1_555 121.1 A SF4 107 B S1 SF4 1_555 A SF4 107 B FE4 SF4 1_555 A SF4 107 B S2 SF4 1_555 101.9 A CYS 20 A SG CYS 20 1_555 A SF4 107 B FE4 SF4 1_555 A SF4 107 B S3 SF4 1_555 116.2 A SF4 107 B S1 SF4 1_555 A SF4 107 B FE4 SF4 1_555 A SF4 107 B S3 SF4 1_555 111.2 A SF4 107 B S2 SF4 1_555 A SF4 107 B FE4 SF4 1_555 A SF4 107 B S3 SF4 1_555 101.5 A CYS 39 A SG CYS 39 1_555 A SF4 107 B FE1 SF4 1_555 A SF4 107 B S2 SF4 1_555 115.1 A CYS 39 A SG CYS 39 1_555 A SF4 107 B FE1 SF4 1_555 A SF4 107 B S3 SF4 1_555 116.5 A SF4 107 B S2 SF4 1_555 A SF4 107 B FE1 SF4 1_555 A SF4 107 B S3 SF4 1_555 100.8 A CYS 39 A SG CYS 39 1_555 A SF4 107 B FE1 SF4 1_555 A SF4 107 B S4 SF4 1_555 99.7 A SF4 107 B S2 SF4 1_555 A SF4 107 B FE1 SF4 1_555 A SF4 107 B S4 SF4 1_555 111.3 A SF4 107 B S3 SF4 1_555 A SF4 107 B FE1 SF4 1_555 A SF4 107 B S4 SF4 1_555 114.1 A CYS 42 A SG CYS 42 1_555 A SF4 107 B FE2 SF4 1_555 A SF4 107 B S1 SF4 1_555 104.7 A CYS 42 A SG CYS 42 1_555 A SF4 107 B FE2 SF4 1_555 A SF4 107 B S3 SF4 1_555 115.0 A SF4 107 B S1 SF4 1_555 A SF4 107 B FE2 SF4 1_555 A SF4 107 B S3 SF4 1_555 96.6 A CYS 42 A SG CYS 42 1_555 A SF4 107 B FE2 SF4 1_555 A SF4 107 B S4 SF4 1_555 131.5 A SF4 107 B S1 SF4 1_555 A SF4 107 B FE2 SF4 1_555 A SF4 107 B S4 SF4 1_555 101.8 A SF4 107 B S3 SF4 1_555 A SF4 107 B FE2 SF4 1_555 A SF4 107 B S4 SF4 1_555 101.2 A CYS 45 A SG CYS 45 1_555 A SF4 107 B FE3 SF4 1_555 A SF4 107 B S1 SF4 1_555 95.5 A CYS 45 A SG CYS 45 1_555 A SF4 107 B FE3 SF4 1_555 A SF4 107 B S2 SF4 1_555 121.0 A SF4 107 B S1 SF4 1_555 A SF4 107 B FE3 SF4 1_555 A SF4 107 B S2 SF4 1_555 98.9 A CYS 45 A SG CYS 45 1_555 A SF4 107 B FE3 SF4 1_555 A SF4 107 B S4 SF4 1_555 116.2 A SF4 107 B S1 SF4 1_555 A SF4 107 B FE3 SF4 1_555 A SF4 107 B S4 SF4 1_555 119.3 A SF4 107 B S2 SF4 1_555 A SF4 107 B FE3 SF4 1_555 A SF4 107 B S4 SF4 1_555 105.3 A CYS 49 A SG CYS 49 1_555 A F3S 108 C FE4 F3S 1_555 A F3S 108 C S2 F3S 1_555 126.4 A CYS 49 A SG CYS 49 1_555 A F3S 108 C FE4 F3S 1_555 A F3S 108 C S3 F3S 1_555 112.5 A F3S 108 C S2 F3S 1_555 A F3S 108 C FE4 F3S 1_555 A F3S 108 C S3 F3S 1_555 98.8 A CYS 49 A SG CYS 49 1_555 A F3S 108 C FE4 F3S 1_555 A F3S 108 C S4 F3S 1_555 103.8 A F3S 108 C S2 F3S 1_555 A F3S 108 C FE4 F3S 1_555 A F3S 108 C S4 F3S 1_555 112.8 A F3S 108 C S3 F3S 1_555 A F3S 108 C FE4 F3S 1_555 A F3S 108 C S4 F3S 1_555 99.7 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 VAL 3 A O VAL 3 A N PHE 55 A N PHE 55 A O VAL 33 A O VAL 33 A N TYR 26 A N TYR 26 A O PHE 25 A O PHE 25 A N ILE 81 A N ILE 81 1 -3.94 0.60 121.00 117.06 A A A CB CG CD1 TYR TYR TYR 13 13 13 N 1 -13.45 2.20 111.50 98.05 A A A N CA CB VAL VAL VAL 19 19 19 N 1 -12.02 1.70 113.30 101.28 A A A CA CB CG MET MET MET 64 64 64 N 1 5.93 0.80 106.30 112.23 A A A CD1 CG CD2 TRP TRP TRP 78 78 78 N 1 -5.34 0.80 107.30 101.96 A A A CE2 CD2 CG TRP TRP TRP 78 78 78 N 1 5.46 0.80 106.30 111.76 A A A CD1 CG CD2 TRP TRP TRP 94 94 94 N 1 -5.39 0.80 107.30 101.91 A A A CE2 CD2 CG TRP TRP TRP 94 94 94 N 1 -3.26 0.50 120.30 117.04 A A A NE CZ NH2 ARG ARG ARG 106 106 106 N 1 A A NE2 CD2 HIS HIS 103 103 -0.068 0.011 1.373 1.305 N 1 A THR 5 -108.72 -164.44 1 A ASN 30 -148.80 28.55 19.3 MODIFIED PARAMETER AND TOPOLOGY FILES TO REFINE OXIDIZED, DISTORTED [FE-S] CLUSTERS OXIDIZED [FE-S] CLUSTERS WERE REFINED WITH MODIFIED TOPOLOGY AND PARAMETER FILES TO ALLOW FIT OF FE AND S TO DENSITY RESULTING FOR FERRICYANIDE OXIDATION OF THE CRYSTALS. THE RESULTING GEOMETRY IS DISTORTED COMPARED TO IDEAL [FE-S] CLUSTERS. 0.255 0.255 2.1 8.0 7446 88.4 10000000. 0.001 1 0.0 MOLECULAR REPLACEMENT PDB ENTRY 5FD1 2.1 8.0 0 856 15 0 841 0.019 3.19 1.83 2.1 20.0 1AXQ 8124 0.0 0.101 1 11.2 3.9 88.4 2.1 2.25 1.5 3.9 88.4 model building X-PLOR 3.8 refinement X-PLOR 3.8 data reduction XENGEN data scaling XENGEN phasing X-PLOR 3.8 FERRICYANIDE OXIDIZED FDI 1 N N 2 N N 3 N N A ASP 6 A ASP 6 HELX_P A CYS 8 A CYS 8 5 1 3 A ASP 15 A ASP 15 HELX_P A VAL 19 A VAL 19 1 2 5 A GLU 46 A GLU 46 HELX_P A GLU 48 A GLU 48 5 3 3 A GLU 57 A GLU 57 HELX_P A GLU 59 A GLU 59 5 4 3 A GLU 62 A GLU 62 HELX_P A GLU 76 A GLU 76 5 5 15 A ALA 91 A ALA 91 HELX_P A TRP 94 A TRP 94 1 6 4 A LYS 100 A LYS 100 HELX_P A HIS 103 A HIS 103 5 7 4 metalc 2.174 A CYS 8 A SG CYS 8 1_555 A F3S 108 C FE3 F3S 1_555 metalc 2.210 A CYS 16 A SG CYS 16 1_555 A F3S 108 C FE1 F3S 1_555 metalc 2.151 A CYS 20 A SG CYS 20 1_555 A SF4 107 B FE4 SF4 1_555 metalc 2.330 A CYS 39 A SG CYS 39 1_555 A SF4 107 B FE1 SF4 1_555 metalc 2.147 A CYS 42 A SG CYS 42 1_555 A SF4 107 B FE2 SF4 1_555 metalc 2.483 A CYS 45 A SG CYS 45 1_555 A SF4 107 B FE3 SF4 1_555 metalc 2.190 A CYS 49 A SG CYS 49 1_555 A F3S 108 C FE4 F3S 1_555 ELECTRON TRANSPORT ELECTRON TRANSPORT FER1_AZOVI UNP 1 1 P00214 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPN ITEKKDPLPDAEDWDGVKGKLQHLER 1 106 1AXQ 1 106 P00214 A 1 1 106 2 3 anti-parallel anti-parallel anti-parallel A PHE 2 A PHE 2 A VAL 4 A VAL 4 A ILE 54 A ILE 54 A SER 56 A SER 56 A LEU 32 A LEU 32 A ILE 34 A ILE 34 A PHE 25 A PHE 25 A GLU 27 A GLU 27 A PRO 79 A PRO 79 A ILE 81 A ILE 81 BINDING SITE FOR RESIDUE SF4 A 107 A SF4 107 Software 10 BINDING SITE FOR RESIDUE F3S A 108 A F3S 108 Software 10 A PHE 2 A PHE 2 10 1_555 A CYS 20 A CYS 20 10 1_555 A VAL 22 A VAL 22 10 1_555 A CYS 24 A CYS 24 10 1_555 A ILE 34 A ILE 34 10 1_555 A CYS 39 A CYS 39 10 1_555 A ILE 40 A ILE 40 10 1_555 A CYS 42 A CYS 42 10 1_555 A ALA 43 A ALA 43 10 1_555 A CYS 45 A CYS 45 10 1_555 A VAL 4 A VAL 4 10 1_555 A CYS 8 A CYS 8 10 1_555 A LYS 12 A LYS 12 10 1_555 A TYR 13 A TYR 13 10 1_555 A THR 14 A THR 14 10 1_555 A ASP 15 A ASP 15 10 1_555 A CYS 16 A CYS 16 10 1_555 A LEU 32 A LEU 32 10 1_555 A CYS 49 A CYS 49 10 1_555 A ALA 51 A ALA 51 10 1_555 92 P 41 21 2