HEADER DE NOVO PROTEIN 24-MAY-24 9C02 TITLE UIC-1 B7M SOAKED WITH EQUIMOLAR ORTHO-, META-, AND PARA-XYLENE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS SYNTHETIC CONSTRUCT, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.L.HEINZ-KUNERT REVDAT 1 26-NOV-25 9C02 0 JRNL AUTH S.L.HEINZ-KUNERT,A.I.NGUYEN JRNL TITL EVOLVABLE CONFORMATIONAL DIVERSITY IN ASSEMBLIES OF SHORT JRNL TITL 2 PEPTIDES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.7 REMARK 3 NUMBER OF REFLECTIONS : 5048 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.099 REMARK 3 R VALUE (WORKING SET) : 0.081 REMARK 3 FREE R VALUE : 0.100 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 950 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 12.9000 - 1.8500 0.86 1269 138 0.0828 0.0911 REMARK 3 2 1.8500 - 1.4700 0.93 1336 155 0.0770 0.1030 REMARK 3 3 1.4700 - 1.2900 0.81 1182 129 0.0788 0.0913 REMARK 3 4 1.2900 - 1.1700 0.88 1269 143 0.0764 0.0960 REMARK 3 5 1.1600 - 1.0900 0.92 1279 146 0.0727 0.1102 REMARK 3 6 1.0900 - 1.0200 0.77 1113 125 0.0924 0.1227 REMARK 3 7 1.0200 - 0.9700 0.70 1007 114 0.1025 0.1353 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.061 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.694 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 172 REMARK 3 ANGLE : 1.857 232 REMARK 3 CHIRALITY : 0.069 12 REMARK 3 PLANARITY : 0.007 26 REMARK 3 DIHEDRAL : 37.187 25 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9C02 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1000283293. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.688801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5048 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 12.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.1 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.01 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 9.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ACETONITRILE, WATER, SLOW COOLING, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 6.69400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 202 DISTANCE = 7.96 ANGSTROMS DBREF 9C02 A 2 10 PDB 9C02 9C02 2 10 SEQRES 1 A 9 LEU AIB ALA AIB LEU MET GLN AIB LEU HET AIB A 3 13 HET AIB A 5 13 HET AIB A 9 13 HET I77 A 101 29 HET I6W A 102 60 HET OXE A 103 18 HET 8VH A 104 18 HET 8VH A 105 18 HET OXE A 106 18 HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE HETNAM I6W ETHYL 5'-FORMYL[2,2'-BIPYRIDINE]-5-CARBOXYLATE HETNAM OXE ORTHO-XYLENE HETNAM 8VH 1,3-DIMETHYLBENZENE FORMUL 1 AIB 3(C4 H9 N O2) FORMUL 2 I77 C12 H11 N5 O2 FORMUL 3 I6W C14 H12 N2 O4 FORMUL 4 OXE 2(C8 H10) FORMUL 5 8VH 2(C8 H10) FORMUL 8 HOH *2(H2 O) HELIX 1 AA1 LEU A 2 GLN A 8 1 7 LINK C LEU A 2 N AIB A 3 1555 1555 1.34 LINK N LEU A 2 C02AI6W A 102 1555 1555 1.42 LINK N LEU A 2 C02BI6W A 102 1555 1555 1.43 LINK C AIB A 3 N ALA A 4 1555 1555 1.34 LINK C ALA A 4 N AIB A 5 1555 1555 1.33 LINK C AIB A 5 N LEU A 6 1555 1555 1.33 LINK C GLN A 8 N AIB A 9 1555 1555 1.33 LINK C AIB A 9 N ALEU A 10 1555 1555 1.34 LINK C AIB A 9 N BLEU A 10 1555 1555 1.33 LINK C ALEU A 10 N15 I77 A 101 1555 1555 1.42 LINK C BLEU A 10 N15 I77 A 101 1555 1555 1.43 CRYST1 13.789 13.388 27.130 90.00 97.66 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.072522 0.000000 0.009754 0.00000 SCALE2 0.000000 0.074694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037191 0.00000 CONECT 1 215 216 CONECT 3 20 CONECT 20 3 21 26 CONECT 21 20 22 24 25 CONECT 22 21 23 33 CONECT 23 22 CONECT 24 21 27 28 29 CONECT 25 21 30 31 32 CONECT 26 20 CONECT 27 24 CONECT 28 24 CONECT 29 24 CONECT 30 25 CONECT 31 25 CONECT 32 25 CONECT 33 22 CONECT 35 43 CONECT 43 35 44 49 CONECT 44 43 45 47 48 CONECT 45 44 46 56 CONECT 46 45 CONECT 47 44 50 51 52 CONECT 48 44 53 54 55 CONECT 49 43 CONECT 50 47 CONECT 51 47 CONECT 52 47 CONECT 53 48 CONECT 54 48 CONECT 55 48 CONECT 56 45 CONECT 111 126 CONECT 126 111 127 132 CONECT 127 126 128 130 131 CONECT 128 127 129 139 140 CONECT 129 128 CONECT 130 127 133 134 135 CONECT 131 127 136 137 138 CONECT 132 126 CONECT 133 130 CONECT 134 130 CONECT 135 130 CONECT 136 131 CONECT 137 131 CONECT 138 131 CONECT 139 128 CONECT 140 128 CONECT 143 194 CONECT 144 194 CONECT 178 179 192 197 CONECT 179 178 180 181 CONECT 180 179 193 195 CONECT 181 179 182 198 CONECT 182 181 189 199 CONECT 183 184 190 196 CONECT 184 183 185 187 CONECT 185 184 186 200 CONECT 186 185 188 201 CONECT 187 184 191 202 CONECT 188 186 189 191 CONECT 189 182 188 192 CONECT 190 183 203 204 CONECT 191 187 188 CONECT 192 178 189 CONECT 193 180 194 205 CONECT 194 143 144 193 206 CONECT 195 180 CONECT 196 183 CONECT 197 178 CONECT 198 181 CONECT 199 182 CONECT 200 185 CONECT 201 186 CONECT 202 187 CONECT 203 190 CONECT 204 190 CONECT 205 193 CONECT 206 194 CONECT 207 209 219 245 CONECT 208 210 220 246 CONECT 209 207 211 237 CONECT 210 208 212 238 CONECT 211 209 213 235 CONECT 212 210 214 236 CONECT 213 211 223 CONECT 214 212 224 CONECT 215 1 217 239 CONECT 216 1 218 240 CONECT 217 215 219 221 CONECT 218 216 220 222 CONECT 219 207 217 247 CONECT 220 208 218 248 CONECT 221 217 237 249 CONECT 222 218 238 250 CONECT 223 213 225 251 CONECT 224 214 226 252 CONECT 225 223 227 233 CONECT 226 224 228 234 CONECT 227 225 241 243 CONECT 228 226 242 244 CONECT 229 231 241 253 255 CONECT 230 232 242 254 256 CONECT 231 229 257 259 261 CONECT 232 230 258 260 262 CONECT 233 225 235 263 CONECT 234 226 236 264 CONECT 235 211 233 265 CONECT 236 212 234 266 CONECT 237 209 221 CONECT 238 210 222 CONECT 239 215 CONECT 240 216 CONECT 241 227 229 CONECT 242 228 230 CONECT 243 227 CONECT 244 228 CONECT 245 207 CONECT 246 208 CONECT 247 219 CONECT 248 220 CONECT 249 221 CONECT 250 222 CONECT 251 223 CONECT 252 224 CONECT 253 229 CONECT 254 230 CONECT 255 229 CONECT 256 230 CONECT 257 231 CONECT 258 232 CONECT 259 231 CONECT 260 232 CONECT 261 231 CONECT 262 232 CONECT 263 233 CONECT 264 234 CONECT 265 235 CONECT 266 236 CONECT 267 268 272 273 CONECT 268 267 269 274 CONECT 269 268 270 275 CONECT 270 269 271 276 CONECT 271 270 272 277 CONECT 272 267 271 278 CONECT 273 267 279 280 281 CONECT 274 268 282 283 284 CONECT 275 269 CONECT 276 270 CONECT 277 271 CONECT 278 272 CONECT 279 273 CONECT 280 273 CONECT 281 273 CONECT 282 274 CONECT 283 274 CONECT 284 274 CONECT 285 286 290 292 CONECT 286 285 287 293 CONECT 287 286 288 291 CONECT 288 287 289 294 CONECT 289 288 290 295 CONECT 290 285 289 296 CONECT 291 287 297 298 299 CONECT 292 285 300 301 302 CONECT 293 286 CONECT 294 288 CONECT 295 289 CONECT 296 290 CONECT 297 291 CONECT 298 291 CONECT 299 291 CONECT 300 292 CONECT 301 292 CONECT 302 292 CONECT 303 304 308 310 CONECT 304 303 305 311 CONECT 305 304 306 309 CONECT 306 305 307 312 CONECT 307 306 308 313 CONECT 308 303 307 314 CONECT 309 305 315 316 317 CONECT 310 303 318 319 320 CONECT 311 304 CONECT 312 306 CONECT 313 307 CONECT 314 308 CONECT 315 309 CONECT 316 309 CONECT 317 309 CONECT 318 310 CONECT 319 310 CONECT 320 310 CONECT 321 322 326 327 CONECT 322 321 323 328 CONECT 323 322 324 329 CONECT 324 323 325 330 CONECT 325 324 326 331 CONECT 326 321 325 332 CONECT 327 321 333 334 335 CONECT 328 322 336 337 338 CONECT 329 323 CONECT 330 324 CONECT 331 325 CONECT 332 326 CONECT 333 327 CONECT 334 327 CONECT 335 327 CONECT 336 328 CONECT 337 328 CONECT 338 328 MASTER 200 0 9 1 0 0 0 6 136 1 210 1 END