0.030703 0.000000 0.000000 0.000000 0.025100 0.000000 0.000000 0.000000 0.011659 0.00000 0.00000 0.00000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90 90 90 32.57 39.84 85.77 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 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 C5 H11 N O2 Se 196.106 n SELENOMETHIONINE 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 To be published 0353 Crystal structure of probable NifB protein that is involved in FeMo-Co biosynthesis TM1816 from Thermotoga maritima at 1.83 A resolution 10.2210/pdb1o13/pdb pdb_00001o13 100.0 1 CCD 2002-07-05 ADSC QUANTUM 315 DOUBLE CRYSTAL MONOCHROMATOR MAD M x-ray 1 0.97903 1.0 0.91837 1.0 0.97874 1.0 BL9-2 SSRL 0.97903, 0.91837, 0.97874 SYNCHROTRON SSRL BEAMLINE BL9-2 involved in FeMo-Co biosynthesis 15250.700 probable NifB protein 1 man polymer 18.015 water 96 nat water no yes (MSE)GSDKIHHHHHH(MSE)IIAIPVSENRGKDSPISEHFGRAPYFAFVKVKNNAIADISVEENPLAQDHVHGAVPNFV KEKGAELVIVRGIGRRAIAAFEA(MSE)GVKVIKGASGTVEEVVNQYLSGQLKDSDYEVHDHHHHEHH MGSDKIHHHHHHMIIAIPVSENRGKDSPISEHFGRAPYFAFVKVKNNAIADISVEENPLAQDHVHGAVPNFVKEKGAELV IVRGIGRRAIAAFEAMGVKVIKGASGTVEEVVNQYLSGQLKDSDYEVHDHHHHEHH A 283669 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 Thermotoga Escherichia sample TM1816 2336 Thermotoga maritima 562 Escherichia coli 1 2.20 43.55 4.20 0.1M phosphate-citrate 40%(v/v) PEG-600, pH 4.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 4.20 293 Joint Center for Structural Genomics JCSG PSI, Protein Structure Initiative pdbx_unobs_or_zero_occ_atoms software pdbx_database_related database_2 pdbx_unobs_or_zero_occ_atoms struct_conn struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Advisory Refinement description Data collection Database references Advisory Database references Derived calculations 1 0 2002-12-18 1 1 2008-04-26 1 2 2011-07-13 1 3 2017-10-04 1 4 2018-07-18 1 5 2023-01-25 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details Y RCSB Y RCSB 2002-10-15 REL REL HOH water HOH 1 2 HOH HOH 125 A HOH 2 2 HOH HOH 126 A HOH 3 2 HOH HOH 127 A HOH 4 2 HOH HOH 128 A HOH 5 2 HOH HOH 129 A HOH 6 2 HOH HOH 130 A HOH 7 2 HOH HOH 131 A HOH 8 2 HOH HOH 132 A HOH 9 2 HOH HOH 133 A HOH 10 2 HOH HOH 134 A HOH 11 2 HOH HOH 135 A HOH 12 2 HOH HOH 136 A HOH 13 2 HOH HOH 137 A HOH 14 2 HOH HOH 138 A HOH 15 2 HOH HOH 139 A HOH 16 2 HOH HOH 140 A HOH 17 2 HOH HOH 141 A HOH 18 2 HOH HOH 142 A HOH 19 2 HOH HOH 143 A HOH 20 2 HOH HOH 144 A HOH 21 2 HOH HOH 145 A HOH 22 2 HOH HOH 146 A HOH 23 2 HOH HOH 147 A HOH 24 2 HOH HOH 148 A HOH 25 2 HOH HOH 149 A HOH 26 2 HOH HOH 150 A HOH 27 2 HOH HOH 151 A HOH 28 2 HOH HOH 152 A HOH 29 2 HOH HOH 153 A HOH 30 2 HOH HOH 154 A HOH 31 2 HOH HOH 155 A HOH 33 2 HOH HOH 156 A HOH 34 2 HOH HOH 157 A HOH 35 2 HOH HOH 158 A HOH 36 2 HOH HOH 159 A HOH 37 2 HOH HOH 160 A HOH 38 2 HOH HOH 161 A HOH 39 2 HOH HOH 162 A HOH 40 2 HOH HOH 163 A HOH 41 2 HOH HOH 164 A HOH 42 2 HOH HOH 165 A HOH 44 2 HOH HOH 166 A HOH 45 2 HOH HOH 167 A HOH 46 2 HOH HOH 168 A HOH 47 2 HOH HOH 169 A HOH 48 2 HOH HOH 170 A HOH 49 2 HOH HOH 171 A HOH 50 2 HOH HOH 172 A HOH 51 2 HOH HOH 173 A HOH 52 2 HOH HOH 174 A HOH 53 2 HOH HOH 175 A HOH 54 2 HOH HOH 176 A HOH 55 2 HOH HOH 177 A HOH 56 2 HOH HOH 178 A HOH 57 2 HOH HOH 179 A HOH 58 2 HOH HOH 180 A HOH 59 2 HOH HOH 181 A HOH 60 2 HOH HOH 182 A HOH 61 2 HOH HOH 183 A HOH 62 2 HOH HOH 184 A HOH 63 2 HOH HOH 185 A HOH 64 2 HOH HOH 186 A HOH 65 2 HOH HOH 187 A HOH 66 2 HOH HOH 188 A HOH 67 2 HOH HOH 189 A HOH 68 2 HOH HOH 190 A HOH 69 2 HOH HOH 191 A HOH 70 2 HOH HOH 192 A HOH 71 2 HOH HOH 193 A HOH 72 2 HOH HOH 194 A HOH 73 2 HOH HOH 195 A HOH 74 2 HOH HOH 196 A HOH 75 2 HOH HOH 197 A HOH 76 2 HOH HOH 198 A HOH 77 2 HOH HOH 199 A HOH 78 2 HOH HOH 200 A HOH 81 2 HOH HOH 201 A HOH 82 2 HOH HOH 202 A HOH 83 2 HOH HOH 203 A HOH 86 2 HOH HOH 204 A HOH 89 2 HOH HOH 205 A HOH 91 2 HOH HOH 206 A HOH 92 2 HOH HOH 207 A HOH 94 2 HOH HOH 208 A HOH 95 2 HOH HOH 209 A HOH 96 2 HOH HOH 210 A HOH 97 2 HOH HOH 211 A HOH 98 2 HOH HOH 212 A HOH 99 2 HOH HOH 213 A HOH 101 2 HOH HOH 214 A HOH 104 2 HOH HOH 215 A HOH 105 2 HOH HOH 216 A HOH 106 2 HOH HOH 217 A HOH 107 2 HOH HOH 218 A HOH 108 2 HOH HOH 219 A HOH 109 2 HOH HOH 220 A n 1 -11 A n 2 -10 A n 3 -9 A n 4 -8 A n 5 -7 A n 6 -6 A n 7 -5 A n 8 -4 A n 9 -3 A n 10 -2 A n 11 -1 A n 12 0 A MSE 1 n 13 MSE 1 A ILE 2 n 14 ILE 2 A ILE 3 n 15 ILE 3 A ALA 4 n 16 ALA 4 A ILE 5 n 17 ILE 5 A PRO 6 n 18 PRO 6 A VAL 7 n 19 VAL 7 A SER 8 n 20 SER 8 A GLU 9 n 21 GLU 9 A ASN 10 n 22 ASN 10 A ARG 11 n 23 ARG 11 A GLY 12 n 24 GLY 12 A LYS 13 n 25 LYS 13 A ASP 14 n 26 ASP 14 A SER 15 n 27 SER 15 A PRO 16 n 28 PRO 16 A ILE 17 n 29 ILE 17 A SER 18 n 30 SER 18 A GLU 19 n 31 GLU 19 A HIS 20 n 32 HIS 20 A PHE 21 n 33 PHE 21 A GLY 22 n 34 GLY 22 A ARG 23 n 35 ARG 23 A ALA 24 n 36 ALA 24 A PRO 25 n 37 PRO 25 A TYR 26 n 38 TYR 26 A PHE 27 n 39 PHE 27 A ALA 28 n 40 ALA 28 A PHE 29 n 41 PHE 29 A VAL 30 n 42 VAL 30 A LYS 31 n 43 LYS 31 A VAL 32 n 44 VAL 32 A LYS 33 n 45 LYS 33 A ASN 34 n 46 ASN 34 A ASN 35 n 47 ASN 35 A ALA 36 n 48 ALA 36 A ILE 37 n 49 ILE 37 A ALA 38 n 50 ALA 38 A ASP 39 n 51 ASP 39 A ILE 40 n 52 ILE 40 A SER 41 n 53 SER 41 A VAL 42 n 54 VAL 42 A GLU 43 n 55 GLU 43 A GLU 44 n 56 GLU 44 A ASN 45 n 57 ASN 45 A PRO 46 n 58 PRO 46 A LEU 47 n 59 LEU 47 A ALA 48 n 60 ALA 48 A GLN 49 n 61 GLN 49 A ASP 50 n 62 ASP 50 A HIS 51 n 63 HIS 51 A VAL 52 n 64 VAL 52 A HIS 53 n 65 HIS 53 A GLY 54 n 66 GLY 54 A ALA 55 n 67 ALA 55 A VAL 56 n 68 VAL 56 A PRO 57 n 69 PRO 57 A ASN 58 n 70 ASN 58 A PHE 59 n 71 PHE 59 A VAL 60 n 72 VAL 60 A LYS 61 n 73 LYS 61 A GLU 62 n 74 GLU 62 A LYS 63 n 75 LYS 63 A GLY 64 n 76 GLY 64 A ALA 65 n 77 ALA 65 A GLU 66 n 78 GLU 66 A LEU 67 n 79 LEU 67 A VAL 68 n 80 VAL 68 A ILE 69 n 81 ILE 69 A VAL 70 n 82 VAL 70 A ARG 71 n 83 ARG 71 A GLY 72 n 84 GLY 72 A ILE 73 n 85 ILE 73 A GLY 74 n 86 GLY 74 A ARG 75 n 87 ARG 75 A ARG 76 n 88 ARG 76 A ALA 77 n 89 ALA 77 A ILE 78 n 90 ILE 78 A ALA 79 n 91 ALA 79 A ALA 80 n 92 ALA 80 A PHE 81 n 93 PHE 81 A GLU 82 n 94 GLU 82 A ALA 83 n 95 ALA 83 A MSE 84 n 96 MSE 84 A GLY 85 n 97 GLY 85 A VAL 86 n 98 VAL 86 A LYS 87 n 99 LYS 87 A VAL 88 n 100 VAL 88 A ILE 89 n 101 ILE 89 A LYS 90 n 102 LYS 90 A GLY 91 n 103 GLY 91 A ALA 92 n 104 ALA 92 A SER 93 n 105 SER 93 A GLY 94 n 106 GLY 94 A THR 95 n 107 THR 95 A VAL 96 n 108 VAL 96 A GLU 97 n 109 GLU 97 A GLU 98 n 110 GLU 98 A VAL 99 n 111 VAL 99 A VAL 100 n 112 VAL 100 A ASN 101 n 113 ASN 101 A GLN 102 n 114 GLN 102 A TYR 103 n 115 TYR 103 A LEU 104 n 116 LEU 104 A SER 105 n 117 SER 105 A GLY 106 n 118 GLY 106 A GLN 107 n 119 GLN 107 A n 120 108 A n 121 109 A n 122 110 A n 123 111 A n 124 112 A n 125 113 A n 126 114 A n 127 115 A n 128 116 A n 129 117 A n 130 118 A n 131 119 A n 132 120 A n 133 121 A n 134 122 A n 135 123 A n 136 124 A author_defined_assembly 1 monomeric A MSE 1 SELENOMETHIONINE A MSE 13 MET A MSE 84 SELENOMETHIONINE A MSE 96 MET 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 ALA 38 A O ALA 50 A N LYS 31 A N LYS 43 A O VAL 30 A O VAL 42 A N ILE 3 A N ILE 15 A N ALA 4 A N ALA 16 A O LEU 67 A O LEU 79 A N VAL 68 A N VAL 80 A O ILE 89 A O ILE 101 1 A CE MSE 1 A CE MSE 13 0 Y 1 A OE1 GLU 9 A OE1 GLU 21 0 Y 1 A OE2 GLU 9 A OE2 GLU 21 0 Y 1 A CG GLU 19 A CG GLU 31 0 Y 1 A CD GLU 19 A CD GLU 31 0 Y 1 A OE1 GLU 19 A OE1 GLU 31 0 Y 1 A OE2 GLU 19 A OE2 GLU 31 0 Y 1 A CB HIS 20 A CB HIS 32 0 Y 1 A CG HIS 20 A CG HIS 32 0 Y 1 A ND1 HIS 20 A ND1 HIS 32 0 Y 1 A CD2 HIS 20 A CD2 HIS 32 0 Y 1 A CE1 HIS 20 A CE1 HIS 32 0 Y 1 A NE2 HIS 20 A NE2 HIS 32 0 Y 1 A CG ARG 23 A CG ARG 35 0 Y 1 A CD ARG 23 A CD ARG 35 0 Y 1 A NE ARG 23 A NE ARG 35 0 Y 1 A CZ ARG 23 A CZ ARG 35 0 Y 1 A NH1 ARG 23 A NH1 ARG 35 0 Y 1 A NH2 ARG 23 A NH2 ARG 35 0 Y 1 A NZ LYS 31 A NZ LYS 43 0 Y 1 A CG1 VAL 32 A CG1 VAL 44 0 Y 1 A CG LYS 33 A CG LYS 45 0 Y 1 A CD LYS 33 A CD LYS 45 0 Y 1 A CE LYS 33 A CE LYS 45 0 Y 1 A NZ LYS 33 A NZ LYS 45 0 Y 1 A CD GLN 49 A CD GLN 61 0 Y 1 A OE1 GLN 49 A OE1 GLN 61 0 Y 1 A NE2 GLN 49 A NE2 GLN 61 0 Y 1 A OD1 ASP 50 A OD1 ASP 62 0 Y 1 A OD2 ASP 50 A OD2 ASP 62 0 Y 1 A CE LYS 61 A CE LYS 73 0 Y 1 A NZ LYS 61 A NZ LYS 73 0 Y 1 A CG GLU 66 A CG GLU 78 0 Y 1 A CD GLU 66 A CD GLU 78 0 Y 1 A OE1 GLU 66 A OE1 GLU 78 0 Y 1 A OE2 GLU 66 A OE2 GLU 78 0 Y 1 A CG ARG 71 A CG ARG 83 0 Y 1 A CD ARG 71 A CD ARG 83 0 Y 1 A NE ARG 71 A NE ARG 83 0 Y 1 A CZ ARG 71 A CZ ARG 83 0 Y 1 A NH1 ARG 71 A NH1 ARG 83 0 Y 1 A NH2 ARG 71 A NH2 ARG 83 0 Y 1 A CB ARG 75 A CB ARG 87 0 Y 1 A CG ARG 75 A CG ARG 87 0 Y 1 A CD ARG 75 A CD ARG 87 0 Y 1 A NE ARG 75 A NE ARG 87 0 Y 1 A CZ ARG 75 A CZ ARG 87 0 Y 1 A NH1 ARG 75 A NH1 ARG 87 0 Y 1 A NH2 ARG 75 A NH2 ARG 87 0 Y 1 A CG ARG 76 A CG ARG 88 0 Y 1 A CD ARG 76 A CD ARG 88 0 Y 1 A NE ARG 76 A NE ARG 88 0 Y 1 A CZ ARG 76 A CZ ARG 88 0 Y 1 A NH1 ARG 76 A NH1 ARG 88 0 Y 1 A NH2 ARG 76 A NH2 ARG 88 0 Y 1 A CG GLU 82 A CG GLU 94 0 Y 1 A CD GLU 82 A CD GLU 94 0 Y 1 A OE1 GLU 82 A OE1 GLU 94 0 Y 1 A OE2 GLU 82 A OE2 GLU 94 0 Y 1 A CB ALA 83 A CB ALA 95 0 Y 1 A CD LYS 87 A CD LYS 99 0 Y 1 A CE LYS 87 A CE LYS 99 0 Y 1 A NZ LYS 87 A NZ LYS 99 0 Y 1 A CE LYS 90 A CE LYS 102 0 Y 1 A NZ LYS 90 A NZ LYS 102 0 Y 1 A OG SER 93 A OG SER 105 0 Y 1 A MSE -11 A MSE 1 1 Y 1 A GLY -10 A GLY 2 1 Y 1 A SER -9 A SER 3 1 Y 1 A ASP -8 A ASP 4 1 Y 1 A LYS -7 A LYS 5 1 Y 1 A ILE -6 A ILE 6 1 Y 1 A HIS -5 A HIS 7 1 Y 1 A HIS -4 A HIS 8 1 Y 1 A HIS -3 A HIS 9 1 Y 1 A HIS -2 A HIS 10 1 Y 1 A HIS -1 A HIS 11 1 Y 1 A HIS 0 A HIS 12 1 Y 1 A LEU 108 A LEU 120 1 Y 1 A LYS 109 A LYS 121 1 Y 1 A ASP 110 A ASP 122 1 Y 1 A SER 111 A SER 123 1 Y 1 A ASP 112 A ASP 124 1 Y 1 A TYR 113 A TYR 125 1 Y 1 A GLU 114 A GLU 126 1 Y 1 A VAL 115 A VAL 127 1 Y 1 A HIS 116 A HIS 128 1 Y 1 A ASP 117 A ASP 129 1 Y 1 A HIS 118 A HIS 130 1 Y 1 A HIS 119 A HIS 131 1 Y 1 A HIS 120 A HIS 132 1 Y 1 A HIS 121 A HIS 133 1 Y 1 A GLU 122 A GLU 134 1 Y 1 A HIS 123 A HIS 135 1 Y 1 A HIS 124 A HIS 136 1 Y 1 A ARG 71 -97.88 -75.71 26.90 -6.92800 0.00000 0.00000 -2.38300 0.00000 9.31200 THERE WAS NO DENSITY FOR THE FINAL 17 RESIDUES OF THE GENE SEQUENCE. WATERS WERE ADDED TO 3.0+ SIGMA PEAKS IN MFO-DFC MAPS IN APPROPRIATE H-BONDING POSITIONS USING THE CNS WATER_PICK AND WATER_DELETE SCRIPTS 0.241 0.207 0.207 1.83 42.87 498 10351 10351 4.800 99.9 RANDOM 1 ISOTROPIC THROUGHOUT 0.000 MAD ENGH AND HUBER BULK SOLVENT CORRECTION 0.46 243.35 43.00 1.83 42.87 96 904 0 0 808 0.010 1.56 1.454 1.500 2.102 2.000 2.055 2.000 2.914 2.500 0.3684 0.287 1.90 63 1053 9 5.6 24.76 1.830 42.871 1O13 10393 0.089 1 22.3000 14.900 100.0 1.83 1.88 2.300 0.945 7.40 100.0 data reduction MOSFLM data scaling SCALA model building RESOLVE phasing SOLVE refinement CNS 1.0 data scaling CCP4 (SCALA) phasing RESOLVE Crystal structure of a putative dinitrogenase iron-molybdenum cofactor (tm1816) from thermotoga maritima at 1.83 A resolution 1 N N 2 N N A ARG 11 A ARG 23 HELX_P A SER 15 A SER 27 5 1 5 A PRO 46 A PRO 58 HELX_P A GLN 49 A GLN 61 5 2 4 A ALA 55 A ALA 67 HELX_P A LYS 63 A LYS 75 1 3 9 A GLY 74 A GLY 86 HELX_P A MSE 84 A MSE 96 1 4 11 A THR 95 A THR 107 HELX_P A SER 105 A SER 117 1 5 11 covale 1.325 both A MSE 1 A C MSE 13 1_555 A ILE 2 A N ILE 14 1_555 covale 1.330 both A ALA 83 A C ALA 95 1_555 A MSE 84 A N MSE 96 1_555 covale 1.332 both A MSE 84 A C MSE 96 1_555 A GLY 85 A N GLY 97 1_555 BIOSYNTHETIC PROTEIN Ribonuclease h-like motif fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, biosynthetic protein Q9X2D6_THEMA UNP 1 1 Q9X2D6 MIIAIPVSENRGKDSPISEHFGRAPYFAFVKVKNNAIADISVEENPLAQDHVHGAVPNFVKEKGAELVIVRGIGRRAIAA FEAMGVKVIKGASGTVEEVVNQYLSGQLKDSDYEVHDHHHHEHH 1 124 1O13 1 124 Q9X2D6 A 1 13 136 1 expression tag MSE -11 1O13 A Q9X2D6 UNP 1 1 expression tag GLY -10 1O13 A Q9X2D6 UNP 2 1 expression tag SER -9 1O13 A Q9X2D6 UNP 3 1 expression tag ASP -8 1O13 A Q9X2D6 UNP 4 1 expression tag LYS -7 1O13 A Q9X2D6 UNP 5 1 expression tag ILE -6 1O13 A Q9X2D6 UNP 6 1 expression tag HIS -5 1O13 A Q9X2D6 UNP 7 1 expression tag HIS -4 1O13 A Q9X2D6 UNP 8 1 expression tag HIS -3 1O13 A Q9X2D6 UNP 9 1 expression tag HIS -2 1O13 A Q9X2D6 UNP 10 1 expression tag HIS -1 1O13 A Q9X2D6 UNP 11 1 expression tag HIS 0 1O13 A Q9X2D6 UNP 12 1 MET modified residue MSE 1 1O13 A Q9X2D6 UNP 1 13 1 MET modified residue MSE 84 1O13 A Q9X2D6 UNP 84 96 5 anti-parallel anti-parallel parallel parallel A ALA 36 A ALA 48 A GLU 44 A GLU 56 A TYR 26 A TYR 38 A LYS 33 A LYS 45 A ILE 2 A ILE 14 A VAL 7 A VAL 19 A LEU 67 A LEU 79 A ILE 69 A ILE 81 A LYS 87 A LYS 99 A ILE 89 A ILE 101 19 P 21 21 21