0.019380 0.000000 0.000000 0.000000 0.019380 0.000000 0.000000 0.000000 0.007163 0.000000 0.000000 0.000000 SEE REMARK 5 ABOVE. Watenpaugh, K.D. Sieker, L.C. Jensen, L.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 51.600 51.600 139.600 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 C17 H21 N4 O9 P 456.344 FLAVIN MONONUCLEOTIDE RIBOFLAVIN MONOPHOSPHATE 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 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 Elsevier Scientific Publ.Co.,Amsterdam Flavins and Flavoproteins 0991 0-444-41458-4 405 -1 A Crystallographic Structural Study of the Oxidation States of Desulfovibrio Vulgaris Flavodoxin 1976 University Park Press,Baltimore Md. US STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN 32VBAT 0992 0-8391-0764-1 431 Flavin Mononucleotide Conformation and Environment in Flavodoxin from Desulfovibrio Vulgaris 1975 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 70 3857 3860 4521211 The binding of riboflavin-5'-phosphate in a flavoprotein: flavodoxin at 2.0-Angstrom resolution. 1973 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 69 3185 3188 4508313 Structure of the oxidized form of a flavodoxin at 2.5-Angstrom resolution: resolution of the phase ambiguity by anomalous scattering. 1972 US J.Biol.Chem. JBCHA3 0071 0021-9258 252 1453 1463 402366 Amino acid sequence of Desulfovibrio vulgaris flavodoxin. 1977 1 2 3 10.2210/pdb1fx1/pdb pdb_00001fx1 -0.999992 -0.000395 -0.002801 -0.000405 0.999997 0.001799 0.002799 0.001801 -0.999989 0.281225 -0.058360 35.929108 1 x-ray 1 1.0 15833.373 FLAVODOXIN 1 man polymer 456.344 FLAVIN MONONUCLEOTIDE 1 syn non-polymer no no MPKALIVYGSTTGNTEYTAETIARQLANAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEE TGAQGRKVACFGCGDSSYEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAI MPKALIVYGSTTGNTEYTAETIARQLANAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEE TGAQGRKVACFGCGDSSYEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAI 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 n n n n n n n n n n n n n n n n n n n n n n n Desulfovibrio sample 881 Desulfovibrio vulgaris 2.93 58.08 atom_site database_2 database_PDB_matrix pdbx_database_remark pdbx_database_status pdbx_validate_main_chain_plane pdbx_validate_polymer_linkage pdbx_validate_rmsd_angle pdbx_validate_rmsd_bond pdbx_validate_symm_contact pdbx_validate_torsion struct_ref_seq_dif struct_site repository Initial release Coordinates and associated ncs operations (if present) transformed into standard crystal frame repository Remediation Version format compliance Version format compliance Database references Other Advisory Atomic model Data collection Database references Derived calculations Other 1 0 1985-01-02 1 1 2008-03-24 1 2 2011-07-13 1 3 2014-06-25 2 0 2023-07-26 _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _database_2.pdbx_DOI _database_2.pdbx_database_accession _database_PDB_matrix.origx[1][1] _database_PDB_matrix.origx[1][2] _database_PDB_matrix.origx[1][3] _database_PDB_matrix.origx[2][1] _database_PDB_matrix.origx[2][2] _database_PDB_matrix.origx[2][3] _database_PDB_matrix.origx[3][1] _database_PDB_matrix.origx[3][2] _database_PDB_matrix.origx[3][3] _database_PDB_matrix.origx_vector[1] _database_PDB_matrix.origx_vector[2] _database_PDB_matrix.origx_vector[3] _pdbx_database_status.process_site _pdbx_validate_main_chain_plane.improper_torsion_angle _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.dist _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1984-10-15 REL REL FMN FLAVIN MONONUCLEOTIDE FMN 1 2 FMN FMN 149 A n 1 1 A PRO 2 n 2 PRO 2 A LYS 3 n 3 LYS 3 A ALA 4 n 4 ALA 4 A LEU 5 n 5 LEU 5 A ILE 6 n 6 ILE 6 A VAL 7 n 7 VAL 7 A TYR 8 n 8 TYR 8 A GLY 9 n 9 GLY 9 A SER 10 n 10 SER 10 A THR 11 n 11 THR 11 A THR 12 n 12 THR 12 A GLY 13 n 13 GLY 13 A ASN 14 n 14 ASN 14 A THR 15 n 15 THR 15 A GLU 16 n 16 GLU 16 A TYR 17 n 17 TYR 17 A THR 18 n 18 THR 18 A ALA 19 n 19 ALA 19 A GLU 20 n 20 GLU 20 A THR 21 n 21 THR 21 A ILE 22 n 22 ILE 22 A ALA 23 n 23 ALA 23 A ARG 24 n 24 ARG 24 A GLN 25 n 25 GLN 25 A LEU 26 n 26 LEU 26 A ALA 27 n 27 ALA 27 A ASN 28 n 28 ASN 28 A ALA 29 n 29 ALA 29 A GLY 30 n 30 GLY 30 A TYR 31 n 31 TYR 31 A GLU 32 n 32 GLU 32 A VAL 33 n 33 VAL 33 A ASP 34 n 34 ASP 34 A SER 35 n 35 SER 35 A ARG 36 n 36 ARG 36 A ASP 37 n 37 ASP 37 A ALA 38 n 38 ALA 38 A ALA 39 n 39 ALA 39 A SER 40 n 40 SER 40 A VAL 41 n 41 VAL 41 A GLU 42 n 42 GLU 42 A ALA 43 n 43 ALA 43 A GLY 44 n 44 GLY 44 A GLY 45 n 45 GLY 45 A LEU 46 n 46 LEU 46 A PHE 47 n 47 PHE 47 A GLU 48 n 48 GLU 48 A GLY 49 n 49 GLY 49 A PHE 50 n 50 PHE 50 A ASP 51 n 51 ASP 51 A LEU 52 n 52 LEU 52 A VAL 53 n 53 VAL 53 A LEU 54 n 54 LEU 54 A LEU 55 n 55 LEU 55 A GLY 56 n 56 GLY 56 A CYS 57 n 57 CYS 57 A SER 58 n 58 SER 58 A THR 59 n 59 THR 59 A TRP 60 n 60 TRP 60 A GLY 61 n 61 GLY 61 A ASP 62 n 62 ASP 62 A ASP 63 n 63 ASP 63 A SER 64 n 64 SER 64 A ILE 65 n 65 ILE 65 A GLU 66 n 66 GLU 66 A LEU 67 n 67 LEU 67 A GLN 68 n 68 GLN 68 A ASP 69 n 69 ASP 69 A ASP 70 n 70 ASP 70 A PHE 71 n 71 PHE 71 A ILE 72 n 72 ILE 72 A PRO 73 n 73 PRO 73 A LEU 74 n 74 LEU 74 A PHE 75 n 75 PHE 75 A ASP 76 n 76 ASP 76 A SER 77 n 77 SER 77 A LEU 78 n 78 LEU 78 A GLU 79 n 79 GLU 79 A GLU 80 n 80 GLU 80 A THR 81 n 81 THR 81 A GLY 82 n 82 GLY 82 A ALA 83 n 83 ALA 83 A GLN 84 n 84 GLN 84 A GLY 85 n 85 GLY 85 A ARG 86 n 86 ARG 86 A LYS 87 n 87 LYS 87 A VAL 88 n 88 VAL 88 A ALA 89 n 89 ALA 89 A CYS 90 n 90 CYS 90 A PHE 91 n 91 PHE 91 A GLY 92 n 92 GLY 92 A CYS 93 n 93 CYS 93 A GLY 94 n 94 GLY 94 A ASP 95 n 95 ASP 95 A SER 96 n 96 SER 96 A SER 97 n 97 SER 97 A TYR 98 n 98 TYR 98 A GLU 99 n 99 GLU 99 A TYR 100 n 100 TYR 100 A PHE 101 n 101 PHE 101 A CYS 102 n 102 CYS 102 A GLY 103 n 103 GLY 103 A ALA 104 n 104 ALA 104 A VAL 105 n 105 VAL 105 A ASP 106 n 106 ASP 106 A ALA 107 n 107 ALA 107 A ILE 108 n 108 ILE 108 A GLU 109 n 109 GLU 109 A GLU 110 n 110 GLU 110 A LYS 111 n 111 LYS 111 A LEU 112 n 112 LEU 112 A LYS 113 n 113 LYS 113 A ASN 114 n 114 ASN 114 A LEU 115 n 115 LEU 115 A GLY 116 n 116 GLY 116 A ALA 117 n 117 ALA 117 A GLU 118 n 118 GLU 118 A ILE 119 n 119 ILE 119 A VAL 120 n 120 VAL 120 A GLN 121 n 121 GLN 121 A ASP 122 n 122 ASP 122 A GLY 123 n 123 GLY 123 A LEU 124 n 124 LEU 124 A ARG 125 n 125 ARG 125 A ILE 126 n 126 ILE 126 A ASP 127 n 127 ASP 127 A GLY 128 n 128 GLY 128 A ASP 129 n 129 ASP 129 A PRO 130 n 130 PRO 130 A ARG 131 n 131 ARG 131 A ALA 132 n 132 ALA 132 A ALA 133 n 133 ALA 133 A ARG 134 n 134 ARG 134 A ASP 135 n 135 ASP 135 A ASP 136 n 136 ASP 136 A ILE 137 n 137 ILE 137 A VAL 138 n 138 VAL 138 A GLY 139 n 139 GLY 139 A TRP 140 n 140 TRP 140 A ALA 141 n 141 ALA 141 A HIS 142 n 142 HIS 142 A ASP 143 n 143 ASP 143 A VAL 144 n 144 VAL 144 A ARG 145 n 145 ARG 145 A GLY 146 n 146 GLY 146 A ALA 147 n 147 ALA 147 A ILE 148 n 148 ILE 148 A 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 N LEU 124 A N LEU 124 A O CYS 90 A O CYS 90 A O LYS 87 A O LYS 87 A N VAL 53 A N VAL 53 A N LEU 52 A N LEU 52 A O LYS 3 A O LYS 3 A N ALA 4 A N ALA 4 A O GLU 32 A O GLU 32 A N LEU 124 A N LEU 124 A O CYS 90 A O CYS 90 A N VAL 88 A N VAL 88 A O GLU 118 A O GLU 118 A N TRP 60 A N TRP 60 A O GLU 66 A O GLU 66 1 A MET 1 A MET 1 1 Y 1 A A NZ OD1 LYS ASN 111 114 1.41 1 A A O CB ASP ALA 37 38 1.78 1 A ALA 23 -10.45 1 A TYR 31 -14.08 1 A LEU 54 -12.66 1 A GLY 56 -11.43 1 A A C N ALA HIS 141 142 1.20 1 -20.68 1.40 111.50 90.82 A A A CA N CD PRO PRO PRO 2 2 2 N 1 -25.40 2.30 111.70 86.30 A A A CD CE NZ LYS LYS LYS 3 3 3 N 1 -13.82 1.60 122.70 108.88 A A A O C N ALA ALA ARG 23 23 24 Y 1 4.21 0.50 120.30 124.51 A A A NE CZ NH2 ARG ARG ARG 24 24 24 N 1 -4.07 0.60 121.00 116.93 A A A CB CG CD1 TYR TYR TYR 31 31 31 N 1 3.97 0.50 120.30 124.27 A A A NE CZ NH2 ARG ARG ARG 36 36 36 N 1 -37.23 2.50 121.70 84.47 A A A C N CA ASP ALA ALA 37 38 38 Y 1 14.26 1.40 110.10 124.36 A A A N CA CB ALA ALA ALA 38 38 38 N 1 -18.91 2.70 111.00 92.09 A A A N CA C ALA ALA ALA 38 38 38 N 1 -19.13 1.90 110.20 91.07 A A A CB CA C LEU LEU LEU 46 46 46 N 1 17.61 2.00 110.40 128.01 A A A CB CA C PHE PHE PHE 47 47 47 N 1 -31.91 2.00 110.40 78.49 A A A CB CA C GLU GLU GLU 48 48 48 N 1 -14.57 2.20 113.40 98.83 A A A CA CB CG GLU GLU GLU 48 48 48 N 1 -19.64 2.50 121.70 102.06 A A A C N CA GLY CYS CYS 56 57 57 Y 1 16.33 2.20 117.20 133.53 A A A CA C N CYS CYS SER 57 57 58 Y 1 3.79 0.50 120.30 124.09 A A A NE CZ NH2 ARG ARG ARG 86 86 86 N 1 -9.19 1.40 110.10 100.91 A A A N CA CB ALA ALA ALA 107 107 107 N 1 -17.31 1.90 110.20 92.89 A A A CB CA C LEU LEU LEU 112 112 112 N 1 -14.26 2.00 110.40 96.14 A A A N CA CB LEU LEU LEU 112 112 112 N 1 3.96 0.50 120.30 124.26 A A A NE CZ NH2 ARG ARG ARG 125 125 125 N 1 3.34 0.50 120.30 123.64 A A A NE CZ NH2 ARG ARG ARG 131 131 131 N 1 3.95 0.50 120.30 124.25 A A A NE CZ NH2 ARG ARG ARG 134 134 134 N 1 3.72 0.50 120.30 124.02 A A A NE CZ NH2 ARG ARG ARG 145 145 145 N 1 A A CE NZ LYS LYS 3 3 0.969 0.025 1.486 2.455 N 1 A A N CA ALA ALA 38 38 0.512 0.020 1.459 1.971 N 1 A A N CA ALA ALA 39 39 -0.125 0.020 1.459 1.334 N 1 A A CA C LEU LEU 46 46 0.381 0.026 1.525 1.906 N 1 A A N CA PHE PHE 47 47 0.319 0.020 1.459 1.778 N 1 A A CA CB PHE PHE 47 47 -0.202 0.022 1.535 1.333 N 1 A A CA C GLU GLU 48 48 0.696 0.026 1.525 2.221 N 1 A A CA CB PHE PHE 50 50 -0.227 0.022 1.535 1.308 N 1 A A CA C PHE PHE 50 50 0.180 0.026 1.525 1.705 N 1 A A CA C LEU LEU 55 55 -0.293 0.026 1.525 1.232 N 1 A A N CA GLY GLY 56 56 0.117 0.015 1.456 1.573 N 1 A A C N GLY CYS 56 57 0.187 0.023 1.336 1.523 Y 1 A A C N CYS SER 57 58 0.167 0.023 1.336 1.503 Y 1 A A N CA SER SER 58 58 0.149 0.020 1.459 1.608 N 1 A A N CA PHE PHE 75 75 -0.126 0.020 1.459 1.333 N 1 A A N CA ASP ASP 106 106 -0.226 0.020 1.459 1.233 N 1 A A N CA LEU LEU 112 112 0.169 0.020 1.459 1.628 N 1 A A CA CB LEU LEU 112 112 0.187 0.023 1.533 1.720 N 1 A A N CA ILE ILE 137 137 0.124 0.020 1.459 1.583 N 1 A A N CA HIS HIS 142 142 -0.144 0.020 1.459 1.315 N 1 A A CB CG HIS HIS 142 142 -0.104 0.016 1.492 1.388 N 1 A A OD1 CE ASP LYS 95 111 1.56 1_555 6_455 1 A A CG CE ASP LYS 95 111 1.87 1_555 6_455 1 A A OD2 CE ASP LYS 95 111 1.90 1_555 6_455 1 A A OD1 NZ ASP LYS 95 111 1.95 1_555 6_455 1 A A OE1 OE1 GLU GLU 48 48 1.97 1_555 7_555 1 A A OD1 CD ASP LYS 95 111 2.09 1_555 6_455 1 A ALA 38 139.95 -35.09 1 A ALA 43 -20.79 -81.59 1 A ASP 62 72.27 -49.09 1 A ILE 72 -33.26 -78.64 1 A PRO 73 -60.54 95.34 1 A LEU 74 160.29 -39.89 1 A LEU 78 -54.78 -7.21 1 A SER 97 -68.21 -163.47 1 A TYR 98 45.50 144.83 1 A CYS 102 73.63 53.24 1 A ILE 119 -58.95 103.93 SOME OF THE INTERATOMIC DISTANCES ARE SIGNIFICANTLY DIFFERENT FROM THE EXPECTED VALUES. THIS IS MAINLY DUE TO THE FACT THAT THE COORDINATES WERE MANUALLY FITTED TO THE ELECTRON DENSITY AND WERE NOT IDEALIZED OR REFINED. IN PARTICULAR THE FOLLOWING INTERATOMIC DISTANCES DEVIATE SIGNIFICANTLY FROM THE EXPECTED VALUES, RESIDUE RESIDUE ATOM1 - ATOM2 DISTANCE NAME NUMBER LYS 3 CE - NZ 2.455 ALA 38 N - CA 1.972 LEU 46 CA - C 1.905 PHE 47 N - CA 1.778 GLU 48 CA - C 2.221 LEU 55 CA - C 1.232 ASP 106 N - CA 1.233 LEU 112 CB - CA 1.719 2.0 1 2.0 0 1135 31 0 1104 A CRYSTALLOGRAPHIC STRUCTURAL STUDY OF THE OXIDATION STATES OF DESULFOVIBRIO VULGARIS FLAVODOXIN 1 N N 2 N N A GLY 13 A GLY 13 HELX_P A ASN 28 A ASN 28 1 1 16 A PHE 71 A PHE 71 HELX_P A ASP 76 A ASP 76 1 2 6 A CYS 102 A CYS 102 HELX_P A ASN 114 A ASN 114 1 3 13 A ASP 129 A ASP 129 HELX_P A ALA 132 A ALA 132 5 4 4 A ALA 133 A ALA 133 HELX_P A ILE 148 A ILE 148 1 5 16 ELECTRON TRANSFER (FLAVOPROTEIN) ELECTRON TRANSFER (FLAVOPROTEIN) FLAV_DESVH UNP 1 1 P00323 1 148 1FX1 1 148 P00323 A 1 1 148 1 GLU conflict GLN 25 1FX1 A P00323 UNP 25 25 1 ASP conflict ASN 28 1FX1 A P00323 UNP 28 28 5 3 2 parallel parallel parallel parallel parallel parallel anti-parallel A LEU 124 A LEU 124 A ASP 127 A ASP 127 A LYS 87 A LYS 87 A GLY 94 A GLY 94 A LEU 52 A LEU 52 A LEU 55 A LEU 55 A LYS 3 A LYS 3 A VAL 7 A VAL 7 A GLU 32 A GLU 32 A ARG 36 A ARG 36 A LEU 124 A LEU 124 A ASP 127 A ASP 127 A LYS 87 A LYS 87 A GLY 94 A GLY 94 A GLU 118 A GLU 118 A ILE 119 A ILE 119 A THR 59 A THR 59 A TRP 60 A TRP 60 A GLU 66 A GLU 66 A LEU 67 A LEU 67 BINDING SITE FOR RESIDUE FMN A 149 A FMN 149 Software 17 A SER 10 A SER 10 17 1_555 A THR 11 A THR 11 17 1_555 A THR 12 A THR 12 17 1_555 A GLY 13 A GLY 13 17 1_555 A ASN 14 A ASN 14 17 1_555 A THR 15 A THR 15 17 1_555 A ASN 28 A ASN 28 17 3_544 A SER 58 A SER 58 17 1_555 A THR 59 A THR 59 17 1_555 A TRP 60 A TRP 60 17 1_555 A CYS 93 A CYS 93 17 1_555 A GLY 94 A GLY 94 17 1_555 A ASP 95 A ASP 95 17 1_555 A TYR 98 A TYR 98 17 1_555 A TYR 100 A TYR 100 17 1_555 A PHE 101 A PHE 101 17 1_555 A CYS 102 A CYS 102 17 1_555 96 P 43 21 2