0.011227 0.000000 0.000000 0.000000 0.010528 0.000000 0.000000 0.000000 0.018269 0.00000 0.00000 0.00000 Otani, J. Arita, K. Kato, T. Kinoshita, M. Ariyoshi, M. Shirakawa, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 89.074 94.989 54.738 C10 H16 N3 O7 P 321.224 n 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE DNA linking C2 H3 O2 -1 59.044 ACETATE ION 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 C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C2 H6 O2 62.068 1,2-ETHANEDIOL ETHYLENE GLYCOL 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 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 US J.Biol.Chem. JBCHA3 0071 0021-9258 288 6351 6362 10.1074/jbc.M112.431098 23316048 Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4 2013 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 95 1 95 2 CCD 2010-01-27 ADSC QUANTUM 210r CCD 2009-10-14 ADSC QUANTUM 270 SINGLE WAVELENGTH M x-ray 1 SINGLE WAVELENGTH M x-ray 2 1.000 1.0 1.0 BL-5A Photon Factory 1.000 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A AR-NE3A Photon Factory SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 7829.089 Methyl-CpG-binding domain protein 4 3.2.2.- methyl CpG binding domain, UNP residues 69-136 1 man polymer 4263.809 DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3') 1 syn polymer 4326.812 DNA (5'-D(*GP*TP*CP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3') 1 syn polymer 59.044 ACETATE ION 3 syn non-polymer 62.068 1,2-ETHANEDIOL 6 syn non-polymer 18.015 water 154 nat water Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase no no SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG A polypeptide(L) no yes (DG)(DT)(DC)(DA)(DC)(DT)(DA)(DC)(5CM)(DG)(DG)(DA)(DC)(DA) GTCACTACCGGACA B polydeoxyribonucleotide no no (DG)(DT)(DC)(DT)(DG)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DC)(DT) GTCTGGTAGTGACT C polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n mouse sample Mbd4 10090 Mus musculus 562 Escherichia coli BL21(DE3) plasmid 2 3.53 65.11 VAPOR DIFFUSION, HANGING DROP 4.4 pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 VAPOR DIFFUSION, HANGING DROP 4.4 pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 -25.080 1 19 B 1 C 13 -0.391 B_DG1:DC13_C 1 -16.480 -0.225 -0.118 0.035 -10.782 1 20 B 2 C 12 -3.304 B_DT2:DA12_C 2 -7.031 -0.347 0.089 -0.073 -6.211 1 19 B 3 C 11 -1.076 B_DC3:DG11_C 3 -6.081 -0.101 -0.062 -0.219 4.348 1 20 B 4 C 10 0.624 B_DA4:DT10_C 4 -9.707 0.201 0.118 -0.153 4.055 1 19 B 5 C 9 3.769 B_DC5:DG9_C 5 -13.621 0.793 0.117 -0.245 -4.552 1 20 B 6 C 8 1.097 B_DT6:DA8_C 6 -9.780 -0.128 0.127 -0.240 -9.820 1 20 B 7 C 7 0.271 B_DA7:DT7_C 7 -7.266 0.122 0.064 -0.145 -5.872 1 19 B 8 C 6 -1.499 B_DC8:DG6_C 8 -3.950 0.330 0.193 -0.147 -3.950 1 19 B 9 C 5 -0.557 B_5CM9:DG5_C 9 -7.467 0.357 -0.032 -0.134 13.254 1 28 B 10 C 4 -7.293 B_DG10:DT4_C 10 9.223 -2.431 0.269 -0.584 27.737 1 19 B 11 C 3 0.181 B_DG11:DC3_C 11 -0.384 -0.238 0.287 -0.044 24.158 1 20 B 12 C 2 2.402 B_DA12:DT2_C 12 -17.695 0.149 0.179 -0.058 13.623 1 19 B 13 C 1 0.122 B_DC13:DG1_C 13 -15.089 0.334 -0.142 -0.069 2.850 31.960 B B 1 2 6.193 C C 13 12 2.897 3.402 -0.896 -0.664 BB_DG1DT2:DA12DC13_CC 1 -1.467 2.670 31.750 -1.748 1.393 3.206 37.740 B B 2 3 5.653 C C 12 11 3.168 3.647 0.751 0.019 BB_DT2DC3:DG11DA12_CC 2 3.142 -4.870 37.443 -0.432 -0.763 2.993 30.182 B B 3 4 16.977 C C 11 10 3.073 8.717 -0.081 0.160 BB_DC3DA4:DT10DG11_CC 3 -1.289 2.511 28.896 -1.375 -0.093 3.212 33.801 B B 4 5 5.116 C C 10 9 3.278 2.971 0.874 -0.725 BB_DA4DC5:DG9DT10_CC 4 0.323 -0.556 33.673 -1.725 -1.452 3.277 32.760 B B 5 6 8.348 C C 9 8 3.410 4.682 0.124 -0.653 BB_DC5DT6:DA8DG9_CC 5 3.923 -6.994 32.201 -1.990 0.477 3.176 32.985 B B 6 7 13.581 C C 8 7 3.400 7.643 -0.073 -0.589 BB_DT6DA7:DT7DA8_CC 6 0.991 -1.760 32.096 -2.361 0.300 3.221 34.093 B B 7 8 4.272 C C 7 6 3.273 2.502 -0.537 -0.554 BB_DA7DC8:DG6DT7_CC 7 0.222 -0.379 34.003 -1.341 0.951 3.390 30.934 B B 8 9 -3.241 C C 6 5 3.336 -1.725 0.743 -0.060 BB_DC85CM9:DG5DG6_CC 8 3.086 -5.797 30.736 0.232 -0.777 3.099 28.816 B B 9 10 -8.665 C C 5 4 3.204 -4.268 0.110 -0.096 BB_5CM9DG10:DT4DG5_CC 9 -5.786 11.745 27.923 0.742 -1.486 3.139 35.792 B B 10 11 -1.301 C C 4 3 3.177 -0.798 0.296 -0.729 BB_DG10DG11:DC3DT4_CC 10 -4.143 6.756 35.551 -1.074 -1.059 3.423 37.971 B B 11 12 6.114 C C 3 2 3.434 3.962 -0.893 -0.723 BB_DG11DA12:DT2DC3_CC 11 -4.511 6.960 37.510 -1.645 0.765 3.250 33.683 B B 12 13 9.118 C C 2 1 3.498 5.261 0.197 -1.291 BB_DA12DC13:DG1DT2_CC 12 -1.517 2.629 33.248 -3.118 -0.596 repository Initial release Database references 1 0 2013-01-16 1 1 2013-08-14 PDBJ Y PDBJ 2012-09-21 REL REL ACT ACETATE ION EDO 1,2-ETHANEDIOL HOH water ACT 2 4 ACT ACT 201 A ACT 3 4 ACT ACT 202 A EDO 11 5 EDO EDO 203 A EDO 12 5 EDO EDO 204 A EDO 13 5 EDO EDO 205 A EDO 14 5 EDO EDO 206 A EDO 21 5 EDO EDO 207 A ACT 1 4 ACT ACT 101 B EDO 19 5 EDO EDO 101 C HOH 2 6 HOH HOH 301 A HOH 3 6 HOH HOH 302 A HOH 4 6 HOH HOH 303 A HOH 6 6 HOH HOH 304 A HOH 7 6 HOH HOH 305 A HOH 8 6 HOH HOH 306 A HOH 10 6 HOH HOH 307 A HOH 12 6 HOH HOH 308 A HOH 14 6 HOH HOH 309 A HOH 15 6 HOH HOH 310 A HOH 18 6 HOH HOH 311 A HOH 19 6 HOH HOH 312 A HOH 23 6 HOH HOH 313 A HOH 26 6 HOH HOH 314 A HOH 29 6 HOH HOH 315 A HOH 36 6 HOH HOH 316 A HOH 39 6 HOH HOH 317 A HOH 42 6 HOH HOH 318 A HOH 43 6 HOH HOH 319 A HOH 46 6 HOH HOH 320 A HOH 48 6 HOH HOH 321 A HOH 49 6 HOH HOH 322 A HOH 50 6 HOH HOH 323 A HOH 53 6 HOH HOH 324 A HOH 57 6 HOH HOH 325 A HOH 60 6 HOH HOH 326 A HOH 63 6 HOH HOH 327 A HOH 69 6 HOH HOH 328 A HOH 70 6 HOH HOH 329 A HOH 71 6 HOH HOH 330 A HOH 75 6 HOH HOH 331 A HOH 80 6 HOH HOH 332 A HOH 81 6 HOH HOH 333 A HOH 82 6 HOH HOH 334 A HOH 91 6 HOH HOH 335 A HOH 96 6 HOH HOH 336 A HOH 97 6 HOH HOH 337 A HOH 99 6 HOH HOH 338 A HOH 100 6 HOH HOH 339 A HOH 101 6 HOH HOH 340 A HOH 102 6 HOH HOH 341 A HOH 105 6 HOH HOH 342 A HOH 106 6 HOH HOH 343 A HOH 107 6 HOH HOH 344 A HOH 112 6 HOH HOH 345 A HOH 117 6 HOH HOH 346 A HOH 123 6 HOH HOH 347 A HOH 126 6 HOH HOH 348 A HOH 129 6 HOH HOH 349 A HOH 130 6 HOH HOH 350 A HOH 131 6 HOH HOH 351 A HOH 133 6 HOH HOH 352 A HOH 137 6 HOH HOH 353 A HOH 139 6 HOH HOH 354 A HOH 141 6 HOH HOH 355 A HOH 143 6 HOH HOH 356 A HOH 144 6 HOH HOH 357 A HOH 148 6 HOH HOH 358 A HOH 149 6 HOH HOH 359 A HOH 151 6 HOH HOH 360 A HOH 152 6 HOH HOH 361 A HOH 9 6 HOH HOH 362 A HOH 13 6 HOH HOH 201 B HOH 16 6 HOH HOH 202 B HOH 20 6 HOH HOH 203 B HOH 21 6 HOH HOH 204 B HOH 22 6 HOH HOH 205 B HOH 27 6 HOH HOH 206 B HOH 28 6 HOH HOH 207 B HOH 31 6 HOH HOH 208 B HOH 33 6 HOH HOH 209 B HOH 35 6 HOH HOH 210 B HOH 38 6 HOH HOH 211 B HOH 41 6 HOH HOH 212 B HOH 44 6 HOH HOH 213 B HOH 54 6 HOH HOH 214 B HOH 59 6 HOH HOH 215 B HOH 61 6 HOH HOH 216 B HOH 65 6 HOH HOH 217 B HOH 66 6 HOH HOH 218 B HOH 67 6 HOH HOH 219 B HOH 68 6 HOH HOH 220 B HOH 73 6 HOH HOH 221 B HOH 76 6 HOH HOH 222 B HOH 77 6 HOH HOH 223 B HOH 83 6 HOH HOH 224 B HOH 84 6 HOH HOH 225 B HOH 87 6 HOH HOH 226 B HOH 89 6 HOH HOH 227 B HOH 90 6 HOH HOH 228 B HOH 92 6 HOH HOH 229 B HOH 94 6 HOH HOH 230 B HOH 95 6 HOH HOH 231 B HOH 108 6 HOH HOH 232 B HOH 110 6 HOH HOH 233 B HOH 111 6 HOH HOH 234 B HOH 113 6 HOH HOH 235 B HOH 114 6 HOH HOH 236 B HOH 115 6 HOH HOH 237 B HOH 116 6 HOH HOH 238 B HOH 119 6 HOH HOH 239 B HOH 120 6 HOH HOH 240 B HOH 127 6 HOH HOH 241 B HOH 128 6 HOH HOH 242 B HOH 132 6 HOH HOH 243 B HOH 134 6 HOH HOH 244 B HOH 135 6 HOH HOH 245 B HOH 138 6 HOH HOH 246 B HOH 146 6 HOH HOH 247 B HOH 147 6 HOH HOH 248 B HOH 153 6 HOH HOH 249 B HOH 154 6 HOH HOH 250 B HOH 11 6 HOH HOH 251 B HOH 40 6 HOH HOH 201 C HOH 1 6 HOH HOH 202 C HOH 5 6 HOH HOH 203 C HOH 17 6 HOH HOH 204 C HOH 24 6 HOH HOH 205 C HOH 25 6 HOH HOH 206 C HOH 30 6 HOH HOH 207 C HOH 32 6 HOH HOH 208 C HOH 34 6 HOH HOH 209 C HOH 37 6 HOH HOH 210 C HOH 45 6 HOH HOH 211 C HOH 47 6 HOH HOH 212 C HOH 51 6 HOH HOH 213 C HOH 52 6 HOH HOH 214 C HOH 55 6 HOH HOH 215 C HOH 56 6 HOH HOH 216 C HOH 58 6 HOH HOH 217 C HOH 62 6 HOH HOH 218 C HOH 64 6 HOH HOH 219 C HOH 72 6 HOH HOH 220 C HOH 74 6 HOH HOH 221 C HOH 78 6 HOH HOH 222 C HOH 79 6 HOH HOH 223 C HOH 85 6 HOH HOH 224 C HOH 86 6 HOH HOH 225 C HOH 88 6 HOH HOH 226 C HOH 93 6 HOH HOH 227 C HOH 98 6 HOH HOH 228 C HOH 103 6 HOH HOH 229 C HOH 104 6 HOH HOH 230 C HOH 109 6 HOH HOH 231 C HOH 118 6 HOH HOH 232 C HOH 121 6 HOH HOH 233 C HOH 122 6 HOH HOH 234 C HOH 124 6 HOH HOH 235 C HOH 125 6 HOH HOH 236 C HOH 136 6 HOH HOH 237 C HOH 140 6 HOH HOH 238 C HOH 142 6 HOH HOH 239 C HOH 145 6 HOH HOH 240 C HOH 150 6 HOH HOH 241 C n 1 68 A n 2 69 A n 3 70 A LYS 71 n 4 LYS 71 A PRO 72 n 5 PRO 72 A VAL 73 n 6 VAL 73 A PRO 74 n 7 PRO 74 A CYS 75 n 8 CYS 75 A GLY 76 n 9 GLY 76 A TRP 77 n 10 TRP 77 A GLU 78 n 11 GLU 78 A ARG 79 n 12 ARG 79 A VAL 80 n 13 VAL 80 A VAL 81 n 14 VAL 81 A LYS 82 n 15 LYS 82 A GLN 83 n 16 GLN 83 A ARG 84 n 17 ARG 84 A LEU 85 n 18 LEU 85 A SER 86 n 19 SER 86 A GLY 87 n 20 GLY 87 A LYS 88 n 21 LYS 88 A THR 89 n 22 THR 89 A ALA 90 n 23 ALA 90 A GLY 91 n 24 GLY 91 A LYS 92 n 25 LYS 92 A PHE 93 n 26 PHE 93 A ASP 94 n 27 ASP 94 A VAL 95 n 28 VAL 95 A TYR 96 n 29 TYR 96 A PHE 97 n 30 PHE 97 A ILE 98 n 31 ILE 98 A SER 99 n 32 SER 99 A PRO 100 n 33 PRO 100 A GLN 101 n 34 GLN 101 A GLY 102 n 35 GLY 102 A LEU 103 n 36 LEU 103 A LYS 104 n 37 LYS 104 A PHE 105 n 38 PHE 105 A ARG 106 n 39 ARG 106 A SER 107 n 40 SER 107 A LYS 108 n 41 LYS 108 A ARG 109 n 42 ARG 109 A SER 110 n 43 SER 110 A LEU 111 n 44 LEU 111 A ALA 112 n 45 ALA 112 A ASN 113 n 46 ASN 113 A TYR 114 n 47 TYR 114 A LEU 115 n 48 LEU 115 A LEU 116 n 49 LEU 116 A LYS 117 n 50 LYS 117 A ASN 118 n 51 ASN 118 A GLY 119 n 52 GLY 119 A GLU 120 n 53 GLU 120 A THR 121 n 54 THR 121 A PHE 122 n 55 PHE 122 A LEU 123 n 56 LEU 123 A LYS 124 n 57 LYS 124 A PRO 125 n 58 PRO 125 A GLU 126 n 59 GLU 126 A ASP 127 n 60 ASP 127 A PHE 128 n 61 PHE 128 A ASN 129 n 62 ASN 129 A PHE 130 n 63 PHE 130 A THR 131 n 64 THR 131 A VAL 132 n 65 VAL 132 A LEU 133 n 66 LEU 133 A PRO 134 n 67 PRO 134 A LYS 135 n 68 LYS 135 A n 69 136 A DG 1 n 1 DG 1 B DT 2 n 2 DT 2 B DC 3 n 3 DC 3 B DA 4 n 4 DA 4 B DC 5 n 5 DC 5 B DT 6 n 6 DT 6 B DA 7 n 7 DA 7 B DC 8 n 8 DC 8 B 5CM 9 n 9 5CM 9 B DG 10 n 10 DG 10 B DG 11 n 11 DG 11 B DA 12 n 12 DA 12 B DC 13 n 13 DC 13 B DA 14 n 14 DA 14 B DG 1 n 1 DG 1 C DT 2 n 2 DT 2 C DC 3 n 3 DC 3 C DT 4 n 4 DT 4 C DG 5 n 5 DG 5 C DG 6 n 6 DG 6 C DT 7 n 7 DT 7 C DA 8 n 8 DA 8 C DG 9 n 9 DG 9 C DT 10 n 10 DT 10 C DG 11 n 11 DG 11 C DA 12 n 12 DA 12 C DC 13 n 13 DC 13 C DT 14 n 14 DT 14 C 0.6284 -0.4314 0.3256 0.9797 -0.6242 1.5410 0.0083 -0.0141 0.0059 -0.0971 0.0234 -0.0729 0.0997 -0.0137 -0.0487 0.2326 -0.0073 0.0026 0.2517 -0.0245 0.2424 refined -3.3944 -11.8131 4.3750 X-RAY DIFFRACTION 1.7749 1.6014 -0.4628 2.1899 -1.0130 0.5161 -0.0418 -0.2728 0.2781 -0.2738 -0.0546 0.3679 0.1146 0.2262 0.0383 0.3457 -0.0759 -0.0226 0.3937 -0.1141 0.3550 refined -18.9331 -12.0063 -13.7962 X-RAY DIFFRACTION 3.7803 0.2987 0.0373 0.6264 0.3534 0.3422 -0.2650 0.0063 -0.3741 -0.1841 0.1125 0.1463 0.0021 -0.1157 0.1730 0.3022 -0.0426 -0.0095 0.4634 -0.0021 0.3583 refined -22.6605 -13.3668 -11.2981 X-RAY DIFFRACTION A 71 A 135 X-RAY DIFFRACTION 1 chain A B 1 B 14 X-RAY DIFFRACTION 2 chain B C 1 C 14 X-RAY DIFFRACTION 3 chain C author_and_software_defined_assembly PISA 3 trimeric 4670 -8 10660 B 5CM 9 B 5CM 9 DC 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 VAL 80 A N VAL 13 A O TYR 96 A O TYR 29 A N PHE 97 A N PHE 30 A O PHE 105 A O PHE 38 1 A HOH 320 M HOH 1 B HOH 201 N HOH 1 A CG LYS 71 A CG LYS 4 1 Y 1 A CD LYS 71 A CD LYS 4 1 Y 1 A CE LYS 71 A CE LYS 4 1 Y 1 A NZ LYS 71 A NZ LYS 4 1 Y 1 A SER 68 A SER 1 1 Y 1 A GLY 69 A GLY 2 1 Y 1 A HIS 70 A HIS 3 1 Y 1 A GLY 136 A GLY 69 1 Y 1 B B OP2 O DA HOH 4 237 2.19 1 -4.55 0.50 120.30 115.75 A A A NE CZ NH1 ARG ARG ARG 79 79 79 N 1 3.62 0.50 120.30 123.92 A A A NE CZ NH2 ARG ARG ARG 79 79 79 N 1 5.79 0.50 106.80 112.59 B B B O4' C1' C2' DG DG DG 1 1 1 N 1 1.91 0.30 108.30 110.21 B B B O4' C1' N9 DG DG DG 1 1 1 N 1 4.33 0.70 121.90 126.23 B B B N3 C2 O2 DC DC DC 5 5 5 N 1 5.71 0.60 119.00 124.71 B B B C4 C5 C7 DT DT DT 6 6 6 N 1 -5.17 0.60 122.90 117.73 B B B C6 C5 C7 DT DT DT 6 6 6 N 1 -4.73 0.70 108.00 103.27 B B B O4' C1' N1 DC DC DC 8 8 8 N 1 4.71 0.30 108.30 113.01 B B B O4' C1' N9 DG DG DG 11 11 11 N 1 9.80 1.50 119.60 129.40 B B B OP1 P OP2 DA DA DA 14 14 14 N 1 -2.92 0.40 104.50 101.58 B B B O4' C4' C3' DA DA DA 14 14 14 N 1 -5.52 0.80 102.40 96.88 B B B C3' C2' C1' DA DA DA 14 14 14 N 1 3.33 0.50 106.80 110.13 B B B O4' C1' C2' DA DA DA 14 14 14 N 1 2.26 0.30 108.30 110.56 C C C O4' C1' N9 DG DG DG 1 1 1 N 1 -3.66 0.60 127.20 123.54 C C C C2 N3 C4 DT DT DT 2 2 2 N 1 -3.62 0.60 123.70 120.08 C C C C5 C6 N1 DT DT DT 2 2 2 N 1 -3.16 0.50 119.90 116.74 C C C C2 N3 C4 DC DC DC 3 3 3 N 1 -3.13 0.50 121.00 117.87 C C C C5 C6 N1 DC DC DC 3 3 3 N 1 6.08 0.30 108.30 114.38 C C C O4' C1' N1 DT DT DT 4 4 4 N 1 3.35 0.50 111.50 114.85 C C C C5 C6 N1 DG DG DG 5 5 5 N 1 -8.42 1.00 110.10 101.68 C C C C1' O4' C4' DG DG DG 11 11 11 N 1 -4.86 0.80 102.40 97.54 C C C C3' C2' C1' DG DG DG 11 11 11 N 1 2.30 0.30 108.30 110.60 C C C O4' C1' N9 DG DG DG 11 11 11 N 1 -4.43 0.70 124.90 120.47 C C C C5 C4 O4 DT DT DT 14 14 14 N 1 B B O3' C3' DG DG 11 11 -0.051 0.006 1.419 1.368 N 1 B B C6 N1 DA DA 14 14 0.043 0.007 1.351 1.394 N 84.750 40.4743 22.070 -12.9528 0.0000 0.0000 10.7675 -0.0000 2.1853 0.2235 0.1875 0.1892 2.00 23.747 801 16002 5.01 99.44 1.000 0.500 0.30 1 1.34 SAD 24.6200 0.86 1.10 ML FLAT BULK SOLVENT MODEL 54.253 0.342 2.00 23.747 154 1285 36 570 525 0.018 1205 2.071 1728 23.326 479 0.119 185 0.010 123 0.2707 0.2332 2.1240 150 2475 2625 6 100.0000 0.3677 0.2553 2.2879 139 2493 2632 6 99.0000 0.2924 0.2338 2.5179 148 2500 2648 6 100.0000 0.2713 0.2178 2.8817 125 2545 2670 6 100.0000 0.2235 0.1711 3.6286 117 2566 2683 6 100.0000 0.1633 0.1626 23.7489 122 2622 2744 6 98.0000 36.360 2.0 50 3VXV 16110 16062 1 1 0.031 1,2 18.2 7.2 99.7 0.365 2.00 2.07 4.3 1,2 7.3 100 data collection HKL-2000 phasing SOLVE refinement PHENIX (phenix.refine: 1.6.4_486) data reduction HKL-2000 data scaling HKL-2000 Methyl-CpG-binding domain protein 4 (E.C.3.2.2.-)/DNA Crystal structure of methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence 1 N N 2 N N 3 N N 4 N N 4 N N 5 N N 5 N N 5 N N 5 N N 5 N N 4 N N 5 N N 6 N N 6 N N 6 N N A SER 107 A SER 40 HELX_P A GLY 119 A GLY 52 1 1 13 A LYS 124 A LYS 57 HELX_P A PHE 128 A PHE 61 5 2 5 disulf 2.043 A CYS 75 A SG CYS 8 1_555 A CYS 75 A SG CYS 8 3_555 covale 1.603 B DC 8 B O3' DC 8 1_555 B 5CM 9 B P 5CM 9 1_555 covale 1.608 B 5CM 9 B O3' 5CM 9 1_555 B DG 10 B P DG 10 1_555 hydrog WATSON-CRICK B DG 1 B N1 DG 1 1_555 C DC 13 C N3 DC 13 1_555 hydrog WATSON-CRICK B DG 1 B N2 DG 1 1_555 C DC 13 C O2 DC 13 1_555 hydrog WATSON-CRICK B DG 1 B O6 DG 1 1_555 C DC 13 C N4 DC 13 1_555 hydrog WATSON-CRICK B DT 2 B N3 DT 2 1_555 C DA 12 C N1 DA 12 1_555 hydrog WATSON-CRICK B DT 2 B O4 DT 2 1_555 C DA 12 C N6 DA 12 1_555 hydrog WATSON-CRICK B DC 3 B N3 DC 3 1_555 C DG 11 C N1 DG 11 1_555 hydrog WATSON-CRICK B DC 3 B N4 DC 3 1_555 C DG 11 C O6 DG 11 1_555 hydrog WATSON-CRICK B DC 3 B O2 DC 3 1_555 C DG 11 C N2 DG 11 1_555 hydrog WATSON-CRICK B DA 4 B N1 DA 4 1_555 C DT 10 C N3 DT 10 1_555 hydrog WATSON-CRICK B DA 4 B N6 DA 4 1_555 C DT 10 C O4 DT 10 1_555 hydrog WATSON-CRICK B DC 5 B N3 DC 5 1_555 C DG 9 C N1 DG 9 1_555 hydrog WATSON-CRICK B DC 5 B N4 DC 5 1_555 C DG 9 C O6 DG 9 1_555 hydrog WATSON-CRICK B DC 5 B O2 DC 5 1_555 C DG 9 C N2 DG 9 1_555 hydrog WATSON-CRICK B DT 6 B N3 DT 6 1_555 C DA 8 C N1 DA 8 1_555 hydrog WATSON-CRICK B DT 6 B O4 DT 6 1_555 C DA 8 C N6 DA 8 1_555 hydrog WATSON-CRICK B DA 7 B N1 DA 7 1_555 C DT 7 C N3 DT 7 1_555 hydrog WATSON-CRICK B DA 7 B N6 DA 7 1_555 C DT 7 C O4 DT 7 1_555 hydrog WATSON-CRICK B DC 8 B N3 DC 8 1_555 C DG 6 C N1 DG 6 1_555 hydrog WATSON-CRICK B DC 8 B N4 DC 8 1_555 C DG 6 C O6 DG 6 1_555 hydrog WATSON-CRICK B DC 8 B O2 DC 8 1_555 C DG 6 C N2 DG 6 1_555 hydrog WATSON-CRICK B 5CM 9 B N3 5CM 9 1_555 C DG 5 C N1 DG 5 1_555 hydrog WATSON-CRICK B 5CM 9 B N4 5CM 9 1_555 C DG 5 C O6 DG 5 1_555 hydrog WATSON-CRICK B 5CM 9 B O2 5CM 9 1_555 C DG 5 C N2 DG 5 1_555 hydrog TYPE_28_PAIR B DG 10 B N1 DG 10 1_555 C DT 4 C O2 DT 4 1_555 hydrog TYPE_28_PAIR B DG 10 B O6 DG 10 1_555 C DT 4 C N3 DT 4 1_555 hydrog WATSON-CRICK B DG 11 B N1 DG 11 1_555 C DC 3 C N3 DC 3 1_555 hydrog WATSON-CRICK B DG 11 B N2 DG 11 1_555 C DC 3 C O2 DC 3 1_555 hydrog WATSON-CRICK B DG 11 B O6 DG 11 1_555 C DC 3 C N4 DC 3 1_555 hydrog WATSON-CRICK B DA 12 B N1 DA 12 1_555 C DT 2 C N3 DT 2 1_555 hydrog WATSON-CRICK B DA 12 B N6 DA 12 1_555 C DT 2 C O4 DT 2 1_555 hydrog WATSON-CRICK B DC 13 B N3 DC 13 1_555 C DG 1 C N1 DG 1 1_555 hydrog WATSON-CRICK B DC 13 B N4 DC 13 1_555 C DG 1 C O6 DG 1 1_555 hydrog WATSON-CRICK B DC 13 B O2 DC 13 1_555 C DG 1 C N2 DG 1 1_555 HYDROLASE/DNA methyl CpG binding domain, protein-DNA complex, versatile base recognition, HYDROLASE-DNA complex MBD4_MOUSE UNP 1 69 Q9Z2D7 GHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG 3VXV PDB 2 3VXV 3VXV PDB 3 3VXV 69 136 3VXV 69 136 Q9Z2D7 A 1 2 69 1 14 3VXV 1 14 3VXV B 2 1 14 1 14 3VXV 1 14 3VXV C 3 1 14 1 EXPRESSION TAG SER 68 3VXV A Q9Z2D7 UNP 1 3 anti-parallel anti-parallel A GLU 78 A GLU 11 A GLN 83 A GLN 16 A PHE 93 A PHE 26 A ILE 98 A ILE 31 A LYS 104 A LYS 37 A PHE 105 A PHE 38 BINDING SITE FOR RESIDUE ACT A 201 Software 4 BINDING SITE FOR RESIDUE ACT A 202 Software 3 BINDING SITE FOR RESIDUE EDO A 203 Software 5 BINDING SITE FOR RESIDUE EDO A 204 Software 5 BINDING SITE FOR RESIDUE EDO A 205 Software 4 BINDING SITE FOR RESIDUE EDO A 206 Software 3 BINDING SITE FOR RESIDUE EDO A 207 Software 3 BINDING SITE FOR RESIDUE ACT B 101 Software 4 BINDING SITE FOR RESIDUE EDO C 101 Software 3 A GLU 120 A GLU 53 4 1_555 C DC 13 C DC 13 4 8_545 C DT 14 C DT 14 4 6_445 C DT 14 C DT 14 4 8_545 A GLN 101 A GLN 34 3 1_555 A ASN 118 A ASN 51 3 1_555 A GLU 120 A GLU 53 3 1_555 A GLN 83 A GLN 16 5 1_555 A ARG 84 A ARG 17 5 1_555 A HOH 318 M HOH 5 1_555 C DC 3 C DC 3 5 1_555 C DT 4 C DT 4 5 1_555 A GLY 76 A GLY 9 5 1_555 A GLU 78 A GLU 11 5 1_555 A ILE 98 A ILE 31 5 1_555 A SER 99 A SER 32 5 1_555 B DA 14 B DA 14 5 2_555 A CYS 75 A CYS 8 4 1_555 A CYS 75 A CYS 8 4 3_555 A GLY 76 A GLY 9 4 1_555 A TRP 77 A TRP 10 4 1_555 A LYS 104 A LYS 37 3 1_555 A PHE 105 A PHE 38 3 1_555 B ACT 101 K ACT 3 1_555 A VAL 132 A VAL 65 3 1_555 A LEU 133 A LEU 66 3 1_555 A PRO 134 A PRO 67 3 1_555 A EDO 206 I EDO 4 1_555 B 5CM 9 B 5CM 9 4 1_555 B DG 10 B DG 10 4 1_555 B HOH 248 N HOH 4 1_555 B DC 13 B DC 13 3 1_555 C DT 2 C DT 2 3 1_555 C DC 3 C DC 3 3 1_555 20 C 2 2 21