0.017334 0.000000 0.000000 0.000000 0.015788 0.000000 0.000000 0.000000 0.012186 0.000000 0.000000 0.000000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 57.690 63.340 82.060 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 Cl -1 35.453 CHLORIDE ION non-polymer 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 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 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 a DinB-like Protein (NP_389123.1) from BACILLUS SUBTILIS at 2.30 A resolution 10.2210/pdb3dka/pdb pdb_00003dka 100 1 Flat mirror (vertical focusing) CCD 2008-05-14 MARMOSAIC 325 mm CCD Single crystal Si(111) bent monochromator (horizontal focusing) MAD M x-ray 1 0.91837 1.0 0.97956 1.0 0.97904 1.0 BL11-1 SSRL 0.91837,0.97956,0.97904 SYNCHROTRON SSRL BEAMLINE BL11-1 18109.627 DinB-like Protein 2 man polymer 35.453 CHLORIDE ION 1 syn non-polymer 18.015 water 98 nat water no yes G(MSE)CQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETS(MSE)SAEELVKHILTSFHLFANVIKEGNASPFQNKQ EETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLA(MSE)EHEIHHKGNLFVYVRE(MSE)G HTELPFYQQR(MSE) GMCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLN VLAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM A,B 389728 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 n n n n n n n sample NP_389123.1, yjoA, BSU12410 1423 Bacillus subtilis Escherichia Coli HK100 Plasmid SpeedET 1 2.07 40.57 VAPOR DIFFUSION, SITTING DROP 5.6 0.2000M NH4OAc, 30.0000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI, Protein Structure Initiative software software struct_conn database_2 struct_ref_seq_dif repository Initial release Advisory Version format compliance Refinement description Data collection Derived calculations Refinement description Database references 1 0 2008-08-19 1 1 2011-07-13 1 2 2017-10-25 1 3 2019-07-24 1 4 2023-02-01 _software.classification _software.name _software.classification _software.contact_author _software.contact_author_email _software.language _software.location _software.name _software.type _software.version _struct_conn.pdbx_leaving_atom_flag _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details Y RCSB Y RCSB 2008-06-24 REL REL CL CHLORIDE ION HOH water THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. CL 1 2 CL CL 155 A HOH 2 3 HOH HOH 156 A HOH 4 3 HOH HOH 157 A HOH 5 3 HOH HOH 158 A HOH 6 3 HOH HOH 159 A HOH 8 3 HOH HOH 160 A HOH 10 3 HOH HOH 161 A HOH 12 3 HOH HOH 162 A HOH 13 3 HOH HOH 163 A HOH 18 3 HOH HOH 164 A HOH 19 3 HOH HOH 165 A HOH 21 3 HOH HOH 166 A HOH 22 3 HOH HOH 167 A HOH 25 3 HOH HOH 168 A HOH 26 3 HOH HOH 169 A HOH 28 3 HOH HOH 170 A HOH 30 3 HOH HOH 171 A HOH 31 3 HOH HOH 172 A HOH 32 3 HOH HOH 173 A HOH 33 3 HOH HOH 174 A HOH 34 3 HOH HOH 175 A HOH 39 3 HOH HOH 176 A HOH 40 3 HOH HOH 177 A HOH 41 3 HOH HOH 178 A HOH 51 3 HOH HOH 179 A HOH 57 3 HOH HOH 180 A HOH 60 3 HOH HOH 181 A HOH 62 3 HOH HOH 182 A HOH 63 3 HOH HOH 183 A HOH 66 3 HOH HOH 184 A HOH 67 3 HOH HOH 185 A HOH 68 3 HOH HOH 186 A HOH 69 3 HOH HOH 187 A HOH 70 3 HOH HOH 188 A HOH 71 3 HOH HOH 189 A HOH 73 3 HOH HOH 190 A HOH 76 3 HOH HOH 191 A HOH 78 3 HOH HOH 192 A HOH 81 3 HOH HOH 193 A HOH 82 3 HOH HOH 194 A HOH 83 3 HOH HOH 195 A HOH 84 3 HOH HOH 196 A HOH 87 3 HOH HOH 197 A HOH 88 3 HOH HOH 198 A HOH 89 3 HOH HOH 199 A HOH 93 3 HOH HOH 200 A HOH 95 3 HOH HOH 201 A HOH 97 3 HOH HOH 202 A HOH 98 3 HOH HOH 203 A HOH 99 3 HOH HOH 204 A HOH 3 3 HOH HOH 155 B HOH 7 3 HOH HOH 156 B HOH 9 3 HOH HOH 157 B HOH 11 3 HOH HOH 158 B HOH 14 3 HOH HOH 159 B HOH 15 3 HOH HOH 160 B HOH 16 3 HOH HOH 161 B HOH 17 3 HOH HOH 162 B HOH 20 3 HOH HOH 163 B HOH 23 3 HOH HOH 164 B HOH 24 3 HOH HOH 165 B HOH 27 3 HOH HOH 166 B HOH 29 3 HOH HOH 167 B HOH 35 3 HOH HOH 168 B HOH 36 3 HOH HOH 169 B HOH 37 3 HOH HOH 170 B HOH 38 3 HOH HOH 171 B HOH 42 3 HOH HOH 172 B HOH 43 3 HOH HOH 173 B HOH 44 3 HOH HOH 174 B HOH 45 3 HOH HOH 175 B HOH 46 3 HOH HOH 176 B HOH 47 3 HOH HOH 177 B HOH 48 3 HOH HOH 178 B HOH 49 3 HOH HOH 179 B HOH 50 3 HOH HOH 180 B HOH 52 3 HOH HOH 181 B HOH 53 3 HOH HOH 182 B HOH 54 3 HOH HOH 183 B HOH 55 3 HOH HOH 184 B HOH 56 3 HOH HOH 185 B HOH 58 3 HOH HOH 186 B HOH 59 3 HOH HOH 187 B HOH 61 3 HOH HOH 188 B HOH 64 3 HOH HOH 189 B HOH 65 3 HOH HOH 190 B HOH 72 3 HOH HOH 191 B HOH 74 3 HOH HOH 192 B HOH 75 3 HOH HOH 193 B HOH 77 3 HOH HOH 194 B HOH 79 3 HOH HOH 195 B HOH 80 3 HOH HOH 196 B HOH 85 3 HOH HOH 197 B HOH 86 3 HOH HOH 198 B HOH 90 3 HOH HOH 199 B HOH 91 3 HOH HOH 200 B HOH 92 3 HOH HOH 201 B HOH 94 3 HOH HOH 202 B HOH 96 3 HOH HOH 203 B n 1 0 A n 2 1 A n 3 2 A n 4 3 A n 5 4 A ASN 5 n 6 ASN 5 A GLN 6 n 7 GLN 6 A ILE 7 n 8 ILE 7 A VAL 8 n 9 VAL 8 A SER 9 n 10 SER 9 A HIS 10 n 11 HIS 10 A PHE 11 n 12 PHE 11 A LEU 12 n 13 LEU 12 A SER 13 n 14 SER 13 A HIS 14 n 15 HIS 14 A ARG 15 n 16 ARG 15 A ASN 16 n 17 ASN 16 A VAL 17 n 18 VAL 17 A THR 18 n 19 THR 18 A ASN 19 n 20 ASN 19 A GLU 20 n 21 GLU 20 A LEU 21 n 22 LEU 21 A ALA 22 n 23 ALA 22 A GLU 23 n 24 GLU 23 A LYS 24 n 25 LYS 24 A ILE 25 n 26 ILE 25 A SER 26 n 27 SER 26 A LYS 27 n 28 LYS 27 A ASP 28 n 29 ASP 28 A HIS 29 n 30 HIS 29 A TYR 30 n 31 TYR 30 A SER 31 n 32 SER 31 A TYR 32 n 33 TYR 32 A LYS 33 n 34 LYS 33 A PRO 34 n 35 PRO 34 A ALA 35 n 36 ALA 35 A GLU 36 n 37 GLU 36 A THR 37 n 38 THR 37 A SER 38 n 39 SER 38 A MSE 39 n 40 MSE 39 A SER 40 n 41 SER 40 A ALA 41 n 42 ALA 41 A GLU 42 n 43 GLU 42 A GLU 43 n 44 GLU 43 A LEU 44 n 45 LEU 44 A VAL 45 n 46 VAL 45 A LYS 46 n 47 LYS 46 A HIS 47 n 48 HIS 47 A ILE 48 n 49 ILE 48 A LEU 49 n 50 LEU 49 A THR 50 n 51 THR 50 A SER 51 n 52 SER 51 A PHE 52 n 53 PHE 52 A HIS 53 n 54 HIS 53 A LEU 54 n 55 LEU 54 A PHE 55 n 56 PHE 55 A ALA 56 n 57 ALA 56 A ASN 57 n 58 ASN 57 A VAL 58 n 59 VAL 58 A ILE 59 n 60 ILE 59 A LYS 60 n 61 LYS 60 A GLU 61 n 62 GLU 61 A GLY 62 n 63 GLY 62 A ASN 63 n 64 ASN 63 A ALA 64 n 65 ALA 64 A SER 65 n 66 SER 65 A PRO 66 n 67 PRO 66 A PHE 67 n 68 PHE 67 A GLN 68 n 69 GLN 68 A ASN 69 n 70 ASN 69 A n 71 70 A n 72 71 A n 73 72 A n 74 73 A THR 74 n 75 THR 74 A GLU 75 n 76 GLU 75 A THR 76 n 77 THR 76 A ASP 77 n 78 ASP 77 A LEU 78 n 79 LEU 78 A ASN 79 n 80 ASN 79 A VAL 80 n 81 VAL 80 A LEU 81 n 82 LEU 81 A ALA 82 n 83 ALA 82 A LYS 83 n 84 LYS 83 A THR 84 n 85 THR 84 A TYR 85 n 86 TYR 85 A THR 86 n 87 THR 86 A GLU 87 n 88 GLU 87 A LYS 88 n 89 LYS 88 A THR 89 n 90 THR 89 A VAL 90 n 91 VAL 90 A ALA 91 n 92 ALA 91 A ILE 92 n 93 ILE 92 A LEU 93 n 94 LEU 93 A GLU 94 n 95 GLU 94 A GLN 95 n 96 GLN 95 A LEU 96 n 97 LEU 96 A THR 97 n 98 THR 97 A GLU 98 n 99 GLU 98 A GLU 99 n 100 GLU 99 A GLN 100 n 101 GLN 100 A LEU 101 n 102 LEU 101 A ASP 102 n 103 ASP 102 A ARG 103 n 104 ARG 103 A GLU 104 n 105 GLU 104 A ILE 105 n 106 ILE 105 A ASP 106 n 107 ASP 106 A n 108 107 A n 109 108 A n 110 109 A ALA 110 n 111 ALA 110 A PHE 111 n 112 PHE 111 A GLY 112 n 113 GLY 112 A ARG 113 n 114 ARG 113 A LYS 114 n 115 LYS 114 A VAL 115 n 116 VAL 115 A THR 116 n 117 THR 116 A GLY 117 n 118 GLY 117 A ARG 118 n 119 ARG 118 A ALA 119 n 120 ALA 119 A LEU 120 n 121 LEU 120 A LEU 121 n 122 LEU 121 A GLN 122 n 123 GLN 122 A LEU 123 n 124 LEU 123 A ALA 124 n 125 ALA 124 A MSE 125 n 126 MSE 125 A GLU 126 n 127 GLU 126 A HIS 127 n 128 HIS 127 A GLU 128 n 129 GLU 128 A ILE 129 n 130 ILE 129 A HIS 130 n 131 HIS 130 A HIS 131 n 132 HIS 131 A LYS 132 n 133 LYS 132 A GLY 133 n 134 GLY 133 A ASN 134 n 135 ASN 134 A LEU 135 n 136 LEU 135 A PHE 136 n 137 PHE 136 A VAL 137 n 138 VAL 137 A TYR 138 n 139 TYR 138 A VAL 139 n 140 VAL 139 A ARG 140 n 141 ARG 140 A GLU 141 n 142 GLU 141 A MSE 142 n 143 MSE 142 A GLY 143 n 144 GLY 143 A HIS 144 n 145 HIS 144 A THR 145 n 146 THR 145 A GLU 146 n 147 GLU 146 A LEU 147 n 148 LEU 147 A PRO 148 n 149 PRO 148 A PHE 149 n 150 PHE 149 A TYR 150 n 151 TYR 150 A GLN 151 n 152 GLN 151 A GLN 152 n 153 GLN 152 A ARG 153 n 154 ARG 153 A MSE 154 n 155 MSE 154 A n 1 0 B n 2 1 B n 3 2 B n 4 3 B n 5 4 B ASN 5 n 6 ASN 5 B GLN 6 n 7 GLN 6 B ILE 7 n 8 ILE 7 B VAL 8 n 9 VAL 8 B SER 9 n 10 SER 9 B HIS 10 n 11 HIS 10 B PHE 11 n 12 PHE 11 B LEU 12 n 13 LEU 12 B SER 13 n 14 SER 13 B HIS 14 n 15 HIS 14 B ARG 15 n 16 ARG 15 B ASN 16 n 17 ASN 16 B VAL 17 n 18 VAL 17 B THR 18 n 19 THR 18 B ASN 19 n 20 ASN 19 B GLU 20 n 21 GLU 20 B LEU 21 n 22 LEU 21 B ALA 22 n 23 ALA 22 B GLU 23 n 24 GLU 23 B LYS 24 n 25 LYS 24 B ILE 25 n 26 ILE 25 B SER 26 n 27 SER 26 B LYS 27 n 28 LYS 27 B ASP 28 n 29 ASP 28 B HIS 29 n 30 HIS 29 B TYR 30 n 31 TYR 30 B SER 31 n 32 SER 31 B TYR 32 n 33 TYR 32 B LYS 33 n 34 LYS 33 B PRO 34 n 35 PRO 34 B ALA 35 n 36 ALA 35 B GLU 36 n 37 GLU 36 B THR 37 n 38 THR 37 B SER 38 n 39 SER 38 B MSE 39 n 40 MSE 39 B SER 40 n 41 SER 40 B ALA 41 n 42 ALA 41 B GLU 42 n 43 GLU 42 B GLU 43 n 44 GLU 43 B LEU 44 n 45 LEU 44 B VAL 45 n 46 VAL 45 B LYS 46 n 47 LYS 46 B HIS 47 n 48 HIS 47 B ILE 48 n 49 ILE 48 B LEU 49 n 50 LEU 49 B THR 50 n 51 THR 50 B SER 51 n 52 SER 51 B PHE 52 n 53 PHE 52 B HIS 53 n 54 HIS 53 B LEU 54 n 55 LEU 54 B PHE 55 n 56 PHE 55 B ALA 56 n 57 ALA 56 B ASN 57 n 58 ASN 57 B VAL 58 n 59 VAL 58 B ILE 59 n 60 ILE 59 B LYS 60 n 61 LYS 60 B GLU 61 n 62 GLU 61 B GLY 62 n 63 GLY 62 B ASN 63 n 64 ASN 63 B ALA 64 n 65 ALA 64 B SER 65 n 66 SER 65 B PRO 66 n 67 PRO 66 B PHE 67 n 68 PHE 67 B GLN 68 n 69 GLN 68 B ASN 69 n 70 ASN 69 B LYS 70 n 71 LYS 70 B GLN 71 n 72 GLN 71 B GLU 72 n 73 GLU 72 B GLU 73 n 74 GLU 73 B THR 74 n 75 THR 74 B GLU 75 n 76 GLU 75 B THR 76 n 77 THR 76 B ASP 77 n 78 ASP 77 B LEU 78 n 79 LEU 78 B ASN 79 n 80 ASN 79 B VAL 80 n 81 VAL 80 B LEU 81 n 82 LEU 81 B ALA 82 n 83 ALA 82 B LYS 83 n 84 LYS 83 B THR 84 n 85 THR 84 B TYR 85 n 86 TYR 85 B THR 86 n 87 THR 86 B GLU 87 n 88 GLU 87 B LYS 88 n 89 LYS 88 B THR 89 n 90 THR 89 B VAL 90 n 91 VAL 90 B ALA 91 n 92 ALA 91 B ILE 92 n 93 ILE 92 B LEU 93 n 94 LEU 93 B GLU 94 n 95 GLU 94 B GLN 95 n 96 GLN 95 B LEU 96 n 97 LEU 96 B THR 97 n 98 THR 97 B GLU 98 n 99 GLU 98 B GLU 99 n 100 GLU 99 B GLN 100 n 101 GLN 100 B LEU 101 n 102 LEU 101 B ASP 102 n 103 ASP 102 B ARG 103 n 104 ARG 103 B GLU 104 n 105 GLU 104 B ILE 105 n 106 ILE 105 B ASP 106 n 107 ASP 106 B LEU 107 n 108 LEU 107 B THR 108 n 109 THR 108 B n 110 109 B n 111 110 B n 112 111 B n 113 112 B n 114 113 B LYS 114 n 115 LYS 114 B VAL 115 n 116 VAL 115 B THR 116 n 117 THR 116 B GLY 117 n 118 GLY 117 B ARG 118 n 119 ARG 118 B ALA 119 n 120 ALA 119 B LEU 120 n 121 LEU 120 B LEU 121 n 122 LEU 121 B GLN 122 n 123 GLN 122 B LEU 123 n 124 LEU 123 B ALA 124 n 125 ALA 124 B MSE 125 n 126 MSE 125 B GLU 126 n 127 GLU 126 B HIS 127 n 128 HIS 127 B GLU 128 n 129 GLU 128 B ILE 129 n 130 ILE 129 B HIS 130 n 131 HIS 130 B HIS 131 n 132 HIS 131 B LYS 132 n 133 LYS 132 B GLY 133 n 134 GLY 133 B ASN 134 n 135 ASN 134 B LEU 135 n 136 LEU 135 B PHE 136 n 137 PHE 136 B VAL 137 n 138 VAL 137 B TYR 138 n 139 TYR 138 B VAL 139 n 140 VAL 139 B ARG 140 n 141 ARG 140 B GLU 141 n 142 GLU 141 B MSE 142 n 143 MSE 142 B GLY 143 n 144 GLY 143 B HIS 144 n 145 HIS 144 B THR 145 n 146 THR 145 B GLU 146 n 147 GLU 146 B LEU 147 n 148 LEU 147 B PRO 148 n 149 PRO 148 B PHE 149 n 150 PHE 149 B TYR 150 n 151 TYR 150 B GLN 151 n 152 GLN 151 B GLN 152 n 153 GLN 152 B ARG 153 n 154 ARG 153 B n 155 154 B 0.7332 0.2212 -0.2770 1.0220 -0.4726 2.4037 -0.0481 0.0144 0.0834 -0.0617 0.0822 0.1071 -0.1075 -0.1458 -0.0341 -0.0656 0.0059 -0.0026 -0.0319 -0.0036 -0.0223 refined 17.7978 36.2709 18.3858 X-RAY DIFFRACTION 1.3254 -0.3565 -1.5279 0.2585 -0.0198 2.9029 -0.0561 -0.0141 0.0528 0.1019 0.0465 -0.1325 0.0032 0.0979 0.0096 -0.0432 -0.0303 -0.0031 -0.0686 -0.0216 -0.0105 refined 37.8085 37.5655 28.0478 X-RAY DIFFRACTION A 5 A 6 A 154 A 155 X-RAY DIFFRACTION 1 B 5 B 6 B 153 B 154 X-RAY DIFFRACTION 2 author_and_software_defined_assembly PISA 2 dimeric 1880 -11 14180 A MSE 39 SELENOMETHIONINE A MSE 40 MET A MSE 125 SELENOMETHIONINE A MSE 126 MET A MSE 142 SELENOMETHIONINE A MSE 143 MET A MSE 154 SELENOMETHIONINE A MSE 155 MET B MSE 39 SELENOMETHIONINE B MSE 40 MET B MSE 125 SELENOMETHIONINE B MSE 126 MET B MSE 142 SELENOMETHIONINE B MSE 143 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 N ILE 105 A N ILE 106 A O VAL 115 A O VAL 116 B N ILE 105 B N ILE 106 B O VAL 115 B O VAL 116 1 A CD GLN 6 A CD GLN 7 1 Y 1 A OE1 GLN 6 A OE1 GLN 7 1 Y 1 A NE2 GLN 6 A NE2 GLN 7 1 Y 1 A CG ASN 69 A CG ASN 70 1 Y 1 A OD1 ASN 69 A OD1 ASN 70 1 Y 1 A ND2 ASN 69 A ND2 ASN 70 1 Y 1 A OG1 THR 74 A OG1 THR 75 1 Y 1 A CG2 THR 74 A CG2 THR 75 1 Y 1 A CG ASP 106 A CG ASP 107 1 Y 1 A OD1 ASP 106 A OD1 ASP 107 1 Y 1 A OD2 ASP 106 A OD2 ASP 107 1 Y 1 A CG PHE 111 A CG PHE 112 1 Y 1 A CD1 PHE 111 A CD1 PHE 112 1 Y 1 A CD2 PHE 111 A CD2 PHE 112 1 Y 1 A CE1 PHE 111 A CE1 PHE 112 1 Y 1 A CE2 PHE 111 A CE2 PHE 112 1 Y 1 A CZ PHE 111 A CZ PHE 112 1 Y 1 A CD ARG 113 A CD ARG 114 1 Y 1 A NE ARG 113 A NE ARG 114 1 Y 1 A CZ ARG 113 A CZ ARG 114 1 Y 1 A NH1 ARG 113 A NH1 ARG 114 1 Y 1 A NH2 ARG 113 A NH2 ARG 114 1 Y 1 B CG GLN 6 B CG GLN 7 1 Y 1 B CD GLN 6 B CD GLN 7 1 Y 1 B OE1 GLN 6 B OE1 GLN 7 1 Y 1 B NE2 GLN 6 B NE2 GLN 7 1 Y 1 B CG ASN 69 B CG ASN 70 1 Y 1 B OD1 ASN 69 B OD1 ASN 70 1 Y 1 B ND2 ASN 69 B ND2 ASN 70 1 Y 1 B CG LYS 70 B CG LYS 71 1 Y 1 B CD LYS 70 B CD LYS 71 1 Y 1 B CE LYS 70 B CE LYS 71 1 Y 1 B NZ LYS 70 B NZ LYS 71 1 Y 1 B CG GLN 71 B CG GLN 72 1 Y 1 B CD GLN 71 B CD GLN 72 1 Y 1 B OE1 GLN 71 B OE1 GLN 72 1 Y 1 B NE2 GLN 71 B NE2 GLN 72 1 Y 1 B CG GLU 72 B CG GLU 73 1 Y 1 B CD GLU 72 B CD GLU 73 1 Y 1 B OE1 GLU 72 B OE1 GLU 73 1 Y 1 B OE2 GLU 72 B OE2 GLU 73 1 Y 1 B OG1 THR 74 B OG1 THR 75 1 Y 1 B CG2 THR 74 B CG2 THR 75 1 Y 1 B CG LYS 114 B CG LYS 115 1 Y 1 B CD LYS 114 B CD LYS 115 1 Y 1 B CE LYS 114 B CE LYS 115 1 Y 1 B NZ LYS 114 B NZ LYS 115 1 Y 1 B CG ARG 153 B CG ARG 154 1 Y 1 B CD ARG 153 B CD ARG 154 1 Y 1 B NE ARG 153 B NE ARG 154 1 Y 1 B CZ ARG 153 B CZ ARG 154 1 Y 1 B NH1 ARG 153 B NH1 ARG 154 1 Y 1 B NH2 ARG 153 B NH2 ARG 154 1 Y 1 A GLY 0 A GLY 1 1 Y 1 A MSE 1 A MSE 2 1 Y 1 A CYS 2 A CYS 3 1 Y 1 A GLN 3 A GLN 4 1 Y 1 A SER 4 A SER 5 1 Y 1 A LYS 70 A LYS 71 1 Y 1 A GLN 71 A GLN 72 1 Y 1 A GLU 72 A GLU 73 1 Y 1 A GLU 73 A GLU 74 1 Y 1 A LEU 107 A LEU 108 1 Y 1 A THR 108 A THR 109 1 Y 1 A SER 109 A SER 110 1 Y 1 B GLY 0 B GLY 1 1 Y 1 B MSE 1 B MSE 2 1 Y 1 B CYS 2 B CYS 3 1 Y 1 B GLN 3 B GLN 4 1 Y 1 B SER 4 B SER 5 1 Y 1 B SER 109 B SER 110 1 Y 1 B ALA 110 B ALA 111 1 Y 1 B PHE 111 B PHE 112 1 Y 1 B GLY 112 B GLY 113 1 Y 1 B ARG 113 B ARG 114 1 Y 1 B MSE 154 B MSE 155 1 Y 1 A ARG 113 -122.61 -143.72 1 A LYS 114 -173.60 146.20 1 B ASN 69 -69.96 95.31 27.260 2.390 0.000 0.000 -0.470 0.000 -1.920 0.930 0.893 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 0.269 0.217 0.219 2.300 29.566 677 13568 5.000 97.560 15.654 0.193 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0.00 MAD 0.437 0.273 0.800 0.800 1.200 MAXIMUM LIKELIHOOD WITH PHASES MASK 2.300 29.566 98 2387 1 0 2288 0.009 0.021 2343 0.006 0.020 1532 1.073 1.945 3168 0.839 3.000 3763 4.557 5.000 286 33.959 25.043 117 13.550 15.000 418 10.103 15.000 9 0.065 0.200 364 0.003 0.020 2587 0.001 0.020 450 0.192 0.200 519 0.170 0.200 1538 0.172 0.200 1131 0.087 0.200 1140 0.142 0.200 89 0.105 0.200 16 0.225 0.200 18 0.243 0.200 5 1.304 3.000 1511 0.211 3.000 577 2.082 5.000 2308 3.402 8.000 953 4.632 11.000 858 1 A 1 798 X-RAY DIFFRACTION TIGHT POSITIONAL 0.070 0.100 1 A 1 1007 X-RAY DIFFRACTION MEDIUM POSITIONAL 0.250 0.400 1 A 1 798 X-RAY DIFFRACTION TIGHT THERMAL 0.070 0.500 1 A 1 1007 X-RAY DIFFRACTION MEDIUM THERMAL 0.280 1.000 0.289 0.263 2.380 58 1225 1283 15 96.030 34.972 2.30 29.566 3DKA 13596 -3.00 0.097 1 7.300 3.63 95.900 0.571 2.30 2.38 1.58 4548 2313 1 90.50 0.462 2.38 2.48 1.9 5203 2619 1 96.10 0.378 2.48 2.59 2.4 4812 2441 1 96.40 0.280 2.59 2.73 3.0 5069 2554 1 96.00 0.214 2.73 2.90 3.9 4885 2460 1 96.00 0.163 2.90 3.12 5.0 4873 2468 1 97.20 0.107 3.12 3.43 7.6 4973 2501 1 96.80 0.060 3.43 3.93 12.0 4994 2523 1 96.40 0.040 3.93 4.93 16.6 4955 2499 1 97.10 0.035 4.93 29.57 18.5 5051 2562 1 96.50 refinement Murshudov, G.N. ccp4@dl.ac.uk Fortran_77 http://www.ccp4.ac.uk/main.html REFMAC program 5.2.0019 refinement P.D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package phasing George Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html XSCALE package data extraction PDB sw-help@rcsb.rutgers.edu September 10, 2007 C++ http://pdb.rutgers.edu/software/ PDB_EXTRACT package 3.004 data reduction XDS phasing SHELXD phasing autoSHARP Y Crystal structure of a dinb-like protein (yjoa, bsu12410) from bacillus subtilis at 2.30 A resolution 1 N N 1 N N 2 N N 3 N N 3 N N A ASN 5 A ASN 6 HELX_P A GLU 23 A GLU 24 1 1 19 A SER 40 A SER 41 HELX_P A GLY 62 A GLY 63 1 2 23 A ALA 64 A ALA 65 HELX_P A GLN 68 A GLN 69 5 3 5 A ASP 77 A ASP 78 HELX_P A GLN 95 A GLN 96 1 4 19 A THR 97 A THR 98 HELX_P A ARG 103 A ARG 104 1 5 7 A GLY 117 A GLY 118 HELX_P A MSE 142 A MSE 143 1 6 26 B ASN 5 B ASN 6 HELX_P B LYS 24 B LYS 25 1 7 20 B ILE 25 B ILE 26 HELX_P B TYR 30 B TYR 31 5 8 6 B SER 40 B SER 41 HELX_P B GLY 62 B GLY 63 1 9 23 B ALA 64 B ALA 65 HELX_P B GLN 68 B GLN 69 5 10 5 B ASP 77 B ASP 78 HELX_P B GLU 94 B GLU 95 1 11 18 B THR 97 B THR 98 HELX_P B ARG 103 B ARG 104 1 12 7 B GLY 117 B GLY 118 HELX_P B MSE 142 B MSE 143 1 13 26 covale 1.332 both A SER 38 A C SER 39 1_555 A MSE 39 A N MSE 40 1_555 covale 1.328 both A MSE 39 A C MSE 40 1_555 A SER 40 A N SER 41 1_555 covale 1.329 both A ALA 124 A C ALA 125 1_555 A MSE 125 A N MSE 126 1_555 covale 1.329 both A MSE 125 A C MSE 126 1_555 A GLU 126 A N GLU 127 1_555 covale 1.332 both A GLU 141 A C GLU 142 1_555 A MSE 142 A N MSE 143 1_555 covale 1.333 both A MSE 142 A C MSE 143 1_555 A GLY 143 A N GLY 144 1_555 covale 1.334 both A ARG 153 A C ARG 154 1_555 A MSE 154 A N MSE 155 1_555 covale 1.334 both B SER 38 B C SER 39 1_555 B MSE 39 B N MSE 40 1_555 covale 1.326 both B MSE 39 B C MSE 40 1_555 B SER 40 B N SER 41 1_555 covale 1.333 both B ALA 124 B C ALA 125 1_555 B MSE 125 B N MSE 126 1_555 covale 1.325 both B MSE 125 B C MSE 126 1_555 B GLU 126 B N GLU 127 1_555 covale 1.331 both B GLU 141 B C GLU 142 1_555 B MSE 142 B N MSE 143 1_555 covale 1.333 both B MSE 142 B C MSE 143 1_555 B GLY 143 B N GLY 144 1_555 UNKNOWN FUNCTION Dinb/yfit-like putative metalloenzyme fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function A B A B A B A 5 A 5 A 67 A 67 2 B 5 B 5 B 67 B 67 2 A 68 A 68 A 69 A 69 4 B 68 B 68 B 69 B 69 4 A 70 A 70 A 152 A 152 2 B 70 B 70 B 152 B 152 2 YJOA_BACSU UNP 1 1 O34334 MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLNV LAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM 1 154 3DKA 1 154 O34334 A 1 2 155 1 154 3DKA 1 154 O34334 B 1 2 155 1 expression tag GLY 0 3DKA A O34334 UNP 1 2 expression tag GLY 0 3DKA B O34334 UNP 1 2 2 anti-parallel anti-parallel A GLU 104 A GLU 105 A ILE 105 A ILE 106 A VAL 115 A VAL 116 A THR 116 A THR 117 B GLU 104 B GLU 105 B ILE 105 B ILE 106 B VAL 115 B VAL 116 B THR 116 B THR 117 19 P 21 21 21