0.010051 0.000000 0.000000 0.000000 0.010051 0.000000 0.000000 0.000000 0.021789 0.00000 0.00000 0.00000 Vivekanandan, S. Moovarkumudalvan, B. Lescar, J. Kolatkar, P.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 99.492 99.492 45.894 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 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 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 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 N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N O N 75 N P N 76 N O N 77 N O N 78 N O N 79 N C N 80 R C N 81 N O N 82 S C N 83 N O N 84 N C N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C Y 90 N C N 91 N N Y 92 N N Y 93 N C Y 94 N N Y 95 N C N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N O N 111 N P N 112 N O N 113 N O N 114 N O N 115 N C N 116 R C N 117 N O N 118 S C N 119 N O N 120 N C N 121 R C N 122 N N N 123 N C N 124 N O N 125 N N N 126 N C N 127 N N N 128 N C N 129 N C N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N O N 145 N P N 146 N O N 147 N O N 148 N O N 149 N C N 150 R C N 151 N O N 152 S C N 153 N O N 154 N C N 155 R C Y 156 N N Y 157 N C Y 158 N N Y 159 N C N 160 N C N 161 N O N 162 N N N 163 N C N 164 N N N 165 N N Y 166 N C N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N O N 182 N P N 183 N O N 184 N O N 185 N O N 186 N C N 187 R C N 188 N O N 189 S C N 190 N O N 191 N C N 192 R C N 193 N N N 194 N C N 195 N O N 196 N N N 197 N C N 198 N O N 199 N C N 200 N C N 201 N C N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N N N 218 S C N 219 N C N 220 N O N 221 N C N 222 N C N 223 N C N 224 N O N 225 N N N 226 N O N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N N N 238 S C N 239 N C N 240 N O N 241 N C N 242 N C N 243 N C N 244 N O N 245 N O N 246 N O N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N N N 257 N C N 258 N C N 259 N O N 260 N O N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N N N 267 S C N 268 N C N 269 N O N 270 N C Y 271 N C Y 272 N N Y 273 N C Y 274 N C Y 275 N N N 276 N O N 277 N H N 278 N H N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N O N 288 N H N 289 N H N 290 N N N 291 S C N 292 N C N 293 N O N 294 N C N 295 N C N 296 N C N 297 N C N 298 N O N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H N 312 N N N 313 S C N 314 N C N 315 N O N 316 N C N 317 N C N 318 N C N 319 N C N 320 N N N 321 N O N 322 N H N 323 N H N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N N N 338 S C N 339 N C N 340 N O N 341 N C N 342 N C N 343 N S N 344 N C N 345 N O N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N N N 358 S C N 359 N C N 360 N O N 361 N C Y 362 N C Y 363 N C Y 364 N C Y 365 N C Y 366 N C Y 367 N C N 368 N O N 369 N H N 370 N H N 371 N H N 372 N H N 373 N H N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N N N 381 S C N 382 N C N 383 N O N 384 N C N 385 N C N 386 N C N 387 N O N 388 N H N 389 N H N 390 N H N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H N 396 N H N 397 N N N 398 S C N 399 N C N 400 N O N 401 N C N 402 N O N 403 N O N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N N N 412 S C N 413 N C N 414 N O N 415 R C N 416 N O N 417 N C N 418 N O N 419 N H N 420 N H N 421 N H N 422 N H N 423 N H N 424 N H N 425 N H N 426 N H N 427 N H N 428 N N N 429 S C N 430 N C N 431 N O N 432 N C Y 433 N C Y 434 N C Y 435 N C Y 436 N N Y 437 N C Y 438 N C Y 439 N C Y 440 N C Y 441 N C N 442 N O N 443 N H N 444 N H N 445 N H N 446 N H N 447 N H N 448 N H N 449 N H N 450 N H N 451 N H N 452 N H N 453 N H N 454 N H N 455 N N N 456 S C N 457 N C N 458 N O N 459 N C Y 460 N C Y 461 N C Y 462 N C Y 463 N C Y 464 N C Y 465 N C N 466 N O N 467 N O N 468 N H N 469 N H N 470 N H N 471 N H N 472 N H N 473 N H N 474 N H N 475 N H N 476 N H N 477 N H N 478 N H N 479 N N N 480 S C N 481 N C N 482 N O N 483 N C N 484 N C N 485 N C N 486 N O N 487 N H N 488 N H N 489 N H N 490 N H N 491 N H N 492 N H N 493 N H N 494 N H N 495 N H N 496 N H N 497 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N doub N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing Y 93 N sing Y 94 N sing Y 95 N doub N 96 N sing Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N doub N 102 N sing N 103 N sing Y 104 N sing Y 105 N doub N 106 N sing Y 107 N sing N 108 N sing N 109 N sing N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N doub N 134 N sing N 135 N doub N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N doub N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing Y 166 N sing Y 167 N sing Y 168 N doub N 169 N sing Y 170 N sing N 171 N sing Y 172 N doub N 173 N doub N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N doub N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N doub N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N doub N 208 N sing N 209 N sing N 210 N sing N 211 N doub N 212 N sing N 213 N sing N 214 N doub N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N doub N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N doub N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N doub N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N doub N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N doub N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N doub N 272 N sing N 273 N sing N 274 N sing N 275 N sing Y 276 N sing Y 277 N doub Y 278 N doub N 279 N sing Y 280 N sing N 281 N sing Y 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N doub N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N doub N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N doub N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N doub N 359 N sing N 360 N sing N 361 N sing N 362 N sing Y 363 N doub Y 364 N sing Y 365 N sing N 366 N sing Y 367 N doub N 368 N sing Y 369 N doub N 370 N sing Y 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N doub N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N sing N 397 N sing N 398 N doub N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N doub N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N doub N 428 N sing N 429 N sing N 430 N sing N 431 N sing Y 432 N doub Y 433 N sing Y 434 N sing N 435 N sing Y 436 N doub Y 437 N sing Y 438 N sing N 439 N sing Y 440 N sing Y 441 N doub N 442 N sing Y 443 N doub N 444 N sing Y 445 N sing N 446 N sing N 447 N sing N 448 N sing N 449 N sing N 450 N sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing N 455 N doub N 456 N sing N 457 N sing N 458 N sing N 459 N sing Y 460 N doub Y 461 N sing Y 462 N sing N 463 N sing Y 464 N doub N 465 N sing Y 466 N doub N 467 N sing Y 468 N sing N 469 N sing N 470 N sing N 471 N sing N 472 N sing N 473 N sing N 474 N sing N 475 N sing N 476 N sing N 477 N sing N 478 N sing N 479 N doub N 480 N sing N 481 N sing N 482 N sing N 483 N sing N 484 N sing N 485 N sing N 486 N sing N 487 N sing N 488 N sing N 489 N sing N 490 N sing To be Published 0353 Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element 10.2210/pdb4s2q/pdb pdb_00004s2q 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2012-08-10 ADSC QUANTUM 315 ROSENBAUM-ROCK DOUBLE CRYSTAL SAGITTAL FOCUSING MONOCHROMATOR SINGLE WAVELENGTH M x-ray 1 1.075 1.0 X29A NSLS 1.075 SYNCHROTRON NSLS BEAMLINE X29A 4871.149 DNA (5'-D(P*AP*GP*GP*CP*TP*TP*TP*GP*TP*TP*CP*TP*CP*CP*TP*G)-3') 1 syn polymer 4965.257 DNA (5'-D(P*AP*GP*GP*AP*GP*AP*AP*CP*AP*AP*AP*GP*CP*CP*TP*G)-3') 1 syn polymer 9264.711 Transcription factor SOX-9 UNP residues 103-178 1 man polymer 18.015 water 2 nat water no no (DA)(DG)(DG)(DC)(DT)(DT)(DT)(DG)(DT)(DT)(DC)(DT)(DC)(DC)(DT)(DG) AGGCTTTGTTCTCCTG A polydeoxyribonucleotide no no (DA)(DG)(DG)(DA)(DG)(DA)(DA)(DC)(DA)(DA)(DA)(DG)(DC)(DC)(DT)(DG) AGGAGAACAAAGCCTG B polydeoxyribonucleotide no no PHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPRR PHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPRR D 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 mouse sample Sox9, Sox-9 10090 Mus musculus 562 Escherichia coli Bl21(DE3) pETG20A pETG20A-Sox9HMG 1 2.97 58.63 VAPOR DIFFUSION, HANGING DROP 8.5 20% PEG 3350, 200mM Sodium/potassium phosphate, 100mM Bis Tris propane, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291K 291 -7.729 1 19 A 4 B 13 -8.089 A_DG4:DC13_B 1 3.707 0.752 -0.393 -0.057 -7.349 1 19 A 5 B 12 -2.252 A_DG5:DC12_B 2 -3.879 0.294 -0.175 0.044 -1.785 1 19 A 6 B 11 -0.131 A_DC6:DG11_B 3 5.971 0.112 -0.031 -0.005 5.366 1 20 A 7 B 10 1.451 A_DT7:DA10_B 4 6.302 -0.578 -0.022 0.072 26.440 1 20 A 8 B 9 2.697 A_DT8:DA9_B 5 9.770 0.155 0.163 0.046 -20.353 1 20 A 9 B 8 1.590 A_DT9:DA8_B 6 -18.446 -0.702 0.097 -0.083 -13.943 1 19 A 10 B 7 5.603 A_DG10:DC7_B 7 -5.504 -0.068 -0.354 0.270 -0.054 1 20 A 11 B 6 -2.001 A_DT11:DA6_B 8 -13.318 -0.001 0.009 -0.140 -1.027 1 20 A 12 B 5 -4.452 A_DT12:DA5_B 9 -5.630 -0.431 0.103 -0.209 -9.490 1 19 A 13 B 4 -2.889 A_DC13:DG4_B 10 -18.921 -0.751 0.255 -0.262 -7.314 1 20 A 14 B 3 -15.144 A_DT14:DA3_B 11 -13.126 0.153 0.107 -0.177 -11.521 1 19 A 15 B 2 -13.193 A_DC15:DG2_B 12 -13.739 -0.339 0.395 -0.307 4.550 1 19 A 16 B 1 -8.535 A_DC16:DG1_B 13 1.573 0.208 -0.238 -0.607 3.278 31.528 A A 4 5 17.285 B B 13 12 3.346 9.193 -0.488 0.156 AA_DG4DG5:DC12DC13_BB 1 -6.561 12.336 29.484 -1.508 -0.382 3.223 30.192 A A 5 6 -1.536 B B 12 11 3.205 -0.800 0.573 -0.132 AA_DG5DC6:DG11DC12_BB 2 0.979 -1.880 30.166 -0.094 -0.904 2.202 29.457 A A 6 7 67.637 B B 11 10 3.599 27.137 0.395 0.845 AA_DC6DT7:DA10DG11_BB 3 2.531 -6.308 11.281 -5.892 -0.073 3.019 31.467 A A 7 8 34.139 B B 10 9 3.261 17.497 0.330 0.569 AA_DT7DT8:DA9DA10_BB 4 -1.687 3.291 26.203 -2.396 -0.941 2.800 56.519 A A 8 9 65.881 B B 9 8 5.423 51.148 -0.255 0.419 AA_DT8DT9:DA8DA9_BB 5 3.626 -4.670 24.623 -4.890 0.648 3.164 38.182 A A 9 10 6.999 B B 8 7 3.076 4.568 0.368 0.976 AA_DT9DG10:DC7DA8_BB 6 -0.390 0.597 37.916 0.940 -0.610 3.258 31.438 A A 10 11 7.664 B B 7 6 3.204 4.129 -0.736 0.098 AA_DG10DT11:DA6DC7_BB 7 -4.166 7.732 30.900 -0.590 0.581 3.059 32.918 A A 11 12 8.072 B B 6 5 3.104 4.558 0.627 -0.353 AA_DT11DT12:DA5DA6_BB 8 1.905 -3.373 32.556 -1.360 -0.798 3.541 34.341 A A 12 13 -2.233 B B 5 4 3.527 -1.317 -0.107 -0.461 AA_DT12DC13:DG4DA5_BB 9 -2.360 4.001 34.237 -0.558 -0.218 3.095 39.964 A A 13 14 16.794 B B 4 3 3.375 11.328 -0.688 -0.423 AA_DC13DT14:DA3DG4_BB 10 1.976 -2.930 38.339 -1.935 1.237 3.222 35.855 A A 14 15 -11.257 B B 3 2 3.314 -6.889 1.053 0.095 AA_DT14DC15:DG2DA3_BB 11 -0.544 0.889 35.204 1.151 -1.789 3.214 31.023 A A 15 16 1.377 B B 2 1 3.095 0.725 0.881 -0.102 AA_DC15DC16:DG1DG2_BB 12 9.553 -18.143 29.542 -0.329 0.171 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Data collection Database references Refinement description 1 0 2016-02-17 1 1 2023-09-20 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2015-01-21 REL REL HOH water 32630 synthetic construct sample 32630 synthetic construct sample 3F27 PDB entry 3F27 PDB experimental model HOH 3 4 HOH HOH 201 D HOH 4 4 HOH HOH 202 D DA 3 n 1 DA 3 A DG 4 n 2 DG 4 A DG 5 n 3 DG 5 A DC 6 n 4 DC 6 A DT 7 n 5 DT 7 A DT 8 n 6 DT 8 A DT 9 n 7 DT 9 A DG 10 n 8 DG 10 A DT 11 n 9 DT 11 A DT 12 n 10 DT 12 A DC 13 n 11 DC 13 A DT 14 n 12 DT 14 A DC 15 n 13 DC 15 A DC 16 n 14 DC 16 A DT 17 n 15 DT 17 A DG 18 n 16 DG 18 A DA 0 n 1 DA 0 B DG 1 n 2 DG 1 B DG 2 n 3 DG 2 B DA 3 n 4 DA 3 B DG 4 n 5 DG 4 B DA 5 n 6 DA 5 B DA 6 n 7 DA 6 B DC 7 n 8 DC 7 B DA 8 n 9 DA 8 B DA 9 n 10 DA 9 B DA 10 n 11 DA 10 B DG 11 n 12 DG 11 B DC 12 n 13 DC 12 B DC 13 n 14 DC 13 B DT 14 n 15 DT 14 B DG 15 n 16 DG 15 B PRO 66 n 1 PRO 66 D HIS 67 n 2 HIS 67 D VAL 68 n 3 VAL 68 D LYS 69 n 4 LYS 69 D ARG 70 n 5 ARG 70 D PRO 71 n 6 PRO 71 D MET 72 n 7 MET 72 D ASN 73 n 8 ASN 73 D ALA 74 n 9 ALA 74 D PHE 75 n 10 PHE 75 D MET 76 n 11 MET 76 D VAL 77 n 12 VAL 77 D TRP 78 n 13 TRP 78 D ALA 79 n 14 ALA 79 D GLN 80 n 15 GLN 80 D ALA 81 n 16 ALA 81 D ALA 82 n 17 ALA 82 D ARG 83 n 18 ARG 83 D ARG 84 n 19 ARG 84 D LYS 85 n 20 LYS 85 D LEU 86 n 21 LEU 86 D ALA 87 n 22 ALA 87 D ASP 88 n 23 ASP 88 D GLN 89 n 24 GLN 89 D TYR 90 n 25 TYR 90 D PRO 91 n 26 PRO 91 D HIS 92 n 27 HIS 92 D LEU 93 n 28 LEU 93 D HIS 94 n 29 HIS 94 D ASN 95 n 30 ASN 95 D ALA 96 n 31 ALA 96 D GLU 97 n 32 GLU 97 D LEU 98 n 33 LEU 98 D SER 99 n 34 SER 99 D LYS 100 n 35 LYS 100 D THR 101 n 36 THR 101 D LEU 102 n 37 LEU 102 D GLY 103 n 38 GLY 103 D LYS 104 n 39 LYS 104 D LEU 105 n 40 LEU 105 D TRP 106 n 41 TRP 106 D ARG 107 n 42 ARG 107 D LEU 108 n 43 LEU 108 D LEU 109 n 44 LEU 109 D ASN 110 n 45 ASN 110 D GLU 111 n 46 GLU 111 D SER 112 n 47 SER 112 D GLU 113 n 48 GLU 113 D LYS 114 n 49 LYS 114 D ARG 115 n 50 ARG 115 D PRO 116 n 51 PRO 116 D PHE 117 n 52 PHE 117 D VAL 118 n 53 VAL 118 D GLU 119 n 54 GLU 119 D GLU 120 n 55 GLU 120 D ALA 121 n 56 ALA 121 D GLU 122 n 57 GLU 122 D ARG 123 n 58 ARG 123 D LEU 124 n 59 LEU 124 D ARG 125 n 60 ARG 125 D VAL 126 n 61 VAL 126 D GLN 127 n 62 GLN 127 D HIS 128 n 63 HIS 128 D LYS 129 n 64 LYS 129 D LYS 130 n 65 LYS 130 D ASP 131 n 66 ASP 131 D HIS 132 n 67 HIS 132 D PRO 133 n 68 PRO 133 D ASP 134 n 69 ASP 134 D TYR 135 n 70 TYR 135 D LYS 136 n 71 LYS 136 D TYR 137 n 72 TYR 137 D GLN 138 n 73 GLN 138 D PRO 139 n 74 PRO 139 D ARG 140 n 75 ARG 140 D ARG 141 n 76 ARG 141 D 2.3093 -0.6000 1.2166 2.4284 1.0806 4.6442 0.3797 0.2757 -0.4596 -0.2644 -0.2457 0.2621 0.5429 -0.2253 -0.1342 0.3766 -0.0053 -0.1381 0.3453 -0.0201 0.4220 refined -16.7256 -0.6508 -0.2605 X-RAY DIFFRACTION 4.1755 2.9486 1.1188 2.7858 2.0884 2.2606 0.2035 -0.4833 -0.3472 -0.1738 0.1518 1.2160 -0.4893 -1.4533 -0.0104 0.5603 0.1756 -0.0429 0.7483 0.0557 0.5124 refined -29.5227 0.3193 1.8315 X-RAY DIFFRACTION 3.5264 0.8023 -0.2317 1.1500 2.2414 4.6476 0.1082 0.4528 -0.5019 -0.2113 0.0520 1.6161 -0.0820 -1.0791 -0.5795 0.6293 0.0167 -0.2352 0.6074 0.1189 0.9497 refined -32.0382 2.5412 -2.4048 X-RAY DIFFRACTION D 66 D 141 X-RAY DIFFRACTION 1 ( CHAIN D AND RESID 66:141 ) B 0 B 15 X-RAY DIFFRACTION 2 ( CHAIN B AND RESID 0:15 ) A 3 A 18 X-RAY DIFFRACTION 3 ( CHAIN A AND RESID 3:18 ) author_and_software_defined_assembly PISA 3 trimeric 4020 -13 10610 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 1 -6.91 0.80 102.40 95.49 A A A C3' C2' C1' DA DA DA 3 3 3 N 1 -3.56 0.40 104.50 100.94 A A A O4' C4' C3' DG DG DG 4 4 4 N 1 -5.08 0.80 102.40 97.32 A A A C3' C2' C1' DG DG DG 4 4 4 N 1 2.84 0.30 108.30 111.14 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 -6.14 1.00 110.10 103.96 A A A C1' O4' C4' DT DT DT 12 12 12 N 1 3.03 0.50 106.80 109.83 A A A O4' C1' C2' DC DC DC 15 15 15 N 1 -6.35 0.80 102.40 96.05 A A A C3' C2' C1' DT DT DT 17 17 17 N 1 3.57 0.30 108.30 111.87 A A A O4' C1' N1 DT DT DT 17 17 17 N 1 4.90 0.60 119.00 123.90 A A A C4 C5 C7 DT DT DT 17 17 17 N 1 -5.95 0.60 122.90 116.95 A A A C6 C5 C7 DT DT DT 17 17 17 N 1 3.24 0.30 108.30 111.54 B B B O4' C1' N9 DG DG DG 2 2 2 N 1 3.89 0.30 108.30 112.19 B B B O4' C1' N9 DA DA DA 3 3 3 N 1 2.36 0.30 108.30 110.66 B B B O4' C1' N9 DA DA DA 5 5 5 N 1 2.44 0.30 108.30 110.74 B B B O4' C1' N9 DA DA DA 8 8 8 N 1 3.31 0.50 106.80 110.11 B B B O4' C1' C2' DA DA DA 9 9 9 N 1 -5.62 0.80 102.40 96.78 B B B C3' C2' C1' DC DC DC 13 13 13 N 1 -9.49 0.80 102.40 92.91 B B B C3' C2' C1' DT DT DT 14 14 14 N 1 5.40 0.30 108.30 113.70 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 6.48 0.60 119.00 125.48 B B B C4 C5 C7 DT DT DT 14 14 14 N 1 -8.20 0.60 122.90 114.70 B B B C6 C5 C7 DT DT DT 14 14 14 N 1 A A O3' C3' DA DA 3 3 -0.051 0.006 1.419 1.368 N 1 D VAL 68 -65.14 -176.38 0.2688 0.2134 0.2162 2.70 24.873 316 6721 6675 4.73 99.69 0.23 RANDOM 1 1.34 MOLECULAR REPLACEMENT 32.56 0.90 1.11 PDB entry 3F27 ML FLAT BULK SOLVENT MODEL 2.70 24.873 2 1314 0 659 653 0.008 1410 1.490 2038 26.547 582 0.069 216 0.005 149 0.4013 0.2581 3.4011 155 3094 100.00 0.2415 0.2028 24.8740 161 3265 100.00 2.7 50.0 4S2Q 6721 6675 0 2 0.133 1 19.0 30.3 99.9 2.7 3.4011 19 6721 0.133 1 30.3 99.9 data collection ADSC Quantum phasing PHASES refinement PHENIX (phenix.refine: 1.8_1069) data reduction HKL-2000 data scaling HKL-2000 Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element 1 N N 2 N N 3 N N 4 N N D ASN 73 C ASN 8 HELX_P D TYR 90 C TYR 25 1 1 18 D HIS 94 C HIS 29 HELX_P D LEU 108 C LEU 43 1 2 15 D ASN 110 C ASN 45 HELX_P D HIS 132 C HIS 67 1 3 23 hydrog WATSON-CRICK A DG 4 A N1 DG 2 1_555 B DC 13 B N3 DC 14 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 2 1_555 B DC 13 B O2 DC 14 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 2 1_555 B DC 13 B N4 DC 14 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 3 1_555 B DC 12 B N3 DC 13 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 3 1_555 B DC 12 B O2 DC 13 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 3 1_555 B DC 12 B N4 DC 13 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 4 1_555 B DG 11 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 4 1_555 B DG 11 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 4 1_555 B DG 11 B N2 DG 12 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 5 1_555 B DA 10 B N1 DA 11 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 5 1_555 B DA 10 B N6 DA 11 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 6 1_555 B DA 9 B N1 DA 10 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 6 1_555 B DA 9 B N6 DA 10 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 7 1_555 B DA 8 B N1 DA 9 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 7 1_555 B DA 8 B N6 DA 9 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 8 1_555 B DC 7 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 8 1_555 B DC 7 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 8 1_555 B DC 7 B N4 DC 8 1_555 hydrog WATSON-CRICK A DT 11 A N3 DT 9 1_555 B DA 6 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 11 A O4 DT 9 1_555 B DA 6 B N6 DA 7 1_555 hydrog WATSON-CRICK A DT 12 A N3 DT 10 1_555 B DA 5 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 12 A O4 DT 10 1_555 B DA 5 B N6 DA 6 1_555 hydrog WATSON-CRICK A DC 13 A N3 DC 11 1_555 B DG 4 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 13 A N4 DC 11 1_555 B DG 4 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 13 A O2 DC 11 1_555 B DG 4 B N2 DG 5 1_555 hydrog WATSON-CRICK A DT 14 A N3 DT 12 1_555 B DA 3 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 14 A O4 DT 12 1_555 B DA 3 B N6 DA 4 1_555 hydrog WATSON-CRICK A DC 15 A N3 DC 13 1_555 B DG 2 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 15 A N4 DC 13 1_555 B DG 2 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 15 A O2 DC 13 1_555 B DG 2 B N2 DG 3 1_555 hydrog WATSON-CRICK A DC 16 A N3 DC 14 1_555 B DG 1 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 16 A N4 DC 14 1_555 B DG 1 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 16 A O2 DC 14 1_555 B DG 1 B N2 DG 2 1_555 DNA BINDING PROTEIN/DNA DNA Bending, Minor groove binding, Transcription Regulation, DNA BINDING PROTEIN-DNA complex SOX9_MOUSE UNP 3 103 Q04887 PHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPRR 4S2Q PDB 1 4S2Q 4S2Q PDB 2 4S2Q 103 178 4S2Q 66 141 Q04887 D 1 1 76 3 18 4S2Q 3 18 4S2Q A 2 1 16 0 15 4S2Q 0 15 4S2Q B 3 1 16 92 P 41 21 2