HEADER RNA 11-MAR-24 8YNO TITLE RNA DUPLEX CONTAINING FORMAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHU)P*CP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS FORMAMIDE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,H.ABE REVDAT 1 20-NOV-24 8YNO 0 JRNL AUTH K.NOMURA,S.AN,Y.KOBAYASHI,J.KONDO,T.SHI,H.MURASE,K.NAKAMOTO, JRNL AUTH 2 Y.KIMURA,N.ABE,K.UI-TEI,H.ABE JRNL TITL SYNTHESIS OF 2'-FORMAMIDONUCLEOSIDE PHOSPHORAMIDITES FOR JRNL TITL 2 SUPPRESSING THE SEED-BASED OFF-TARGET EFFECTS OF SIRNAS. JRNL REF NUCLEIC ACIDS RES. V. 52 10754 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 39231537 JRNL DOI 10.1093/NAR/GKAE741 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.520 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 15137 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1502 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 26.4300 - 2.8900 0.99 1282 144 0.1304 0.1547 REMARK 3 2 2.8900 - 2.2900 1.00 1255 143 0.1812 0.1837 REMARK 3 3 2.2900 - 2.0000 1.00 1242 141 0.1605 0.1721 REMARK 3 4 2.0000 - 1.8200 1.00 1279 140 0.1559 0.1748 REMARK 3 5 1.8200 - 1.6900 1.00 1255 139 0.1364 0.1808 REMARK 3 6 1.6900 - 1.5900 0.99 1239 135 0.1367 0.1727 REMARK 3 7 1.5900 - 1.5100 1.00 1260 134 0.1518 0.1776 REMARK 3 8 1.5100 - 1.4400 1.00 1249 136 0.1541 0.1952 REMARK 3 9 1.4400 - 1.3900 1.00 1241 133 0.1588 0.2019 REMARK 3 10 1.3900 - 1.3400 1.00 1245 138 0.1669 0.1837 REMARK 3 11 1.3400 - 1.3000 0.85 1088 119 0.1714 0.1826 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.55 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8YNO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300046011. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-20 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91962 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15146 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 26.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.449 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.12 REMARK 200 R MERGE FOR SHELL (I) : 0.14600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.510 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 (%): 38.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM CACODYLATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 21.53150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 B 184 DISTANCE = 6.53 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SPM A 101 DBREF 8YNO A 1 12 PDB 8YNO 8YNO 1 12 DBREF 8YNO B 1 12 PDB 8YNO 8YNO 1 12 SEQRES 1 A 12 G G A C 5BU C G A G HHU C C SEQRES 1 B 12 G G A C 5BU C G A G HHU C C HET 5BU A 5 21 HET HHU A 10 22 HET 5BU B 5 21 HET HHU B 10 22 HET SPM A 101 8 HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE HETNAM HHU [(2R,3S,4R,5R)-5-[2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1- HETNAM 2 HHU YL]-4-FORMAMIDO-3-OXIDANYL-OXOLAN-2-YL]METHYL HETNAM 3 HHU DIHYDROGEN PHOSPHATE HETNAM SPM SPERMINE FORMUL 1 5BU 2(C9 H12 BR N2 O9 P) FORMUL 1 HHU 2(C10 H14 N3 O9 P) FORMUL 3 SPM C10 H26 N4 FORMUL 4 HOH *170(H2 O) LINK O3' C A 4 P 5BU A 5 1555 1555 1.61 LINK O3' 5BU A 5 P C A 6 1555 1555 1.60 LINK O3' G A 9 P HHU A 10 1555 1555 1.61 LINK O3' HHU A 10 P C A 11 1555 1555 1.60 LINK O3' C B 4 P 5BU B 5 1555 1555 1.61 LINK O3' 5BU B 5 P C B 6 1555 1555 1.60 LINK O3' G B 9 P HHU B 10 1555 1555 1.60 LINK O3' HHU B 10 P C B 11 1555 1555 1.59 CRYST1 27.633 43.063 28.043 90.00 109.51 90.00 P 1 21 1 4 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 0.036189 0.000000 0.012824 0.00000 SCALE2 0.000000 0.023222 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037832 0.00000 CONECT 74 86 CONECT 86 74 87 88 89 CONECT 87 86 CONECT 88 86 CONECT 89 86 90 CONECT 90 89 91 CONECT 91 90 92 93 CONECT 92 91 97 CONECT 93 91 94 95 CONECT 94 93 107 CONECT 95 93 96 97 CONECT 96 95 CONECT 97 92 95 98 CONECT 98 97 99 105 CONECT 99 98 100 101 CONECT 100 99 CONECT 101 99 102 CONECT 102 101 103 104 CONECT 103 102 CONECT 104 102 105 106 CONECT 105 98 104 CONECT 106 104 CONECT 107 94 CONECT 180 216 CONECT 195 197 205 211 CONECT 196 205 207 208 CONECT 197 195 198 206 CONECT 198 197 200 209 CONECT 199 201 207 210 CONECT 200 198 202 211 CONECT 201 199 203 CONECT 202 200 212 CONECT 203 201 205 CONECT 204 206 213 CONECT 205 195 196 203 CONECT 206 197 204 CONECT 207 196 199 CONECT 208 196 CONECT 209 198 217 CONECT 210 199 CONECT 211 195 200 CONECT 212 202 216 CONECT 213 204 CONECT 214 216 CONECT 215 216 CONECT 216 180 212 214 215 CONECT 217 209 CONECT 331 343 CONECT 343 331 344 345 346 CONECT 344 343 CONECT 345 343 CONECT 346 343 347 CONECT 347 346 348 CONECT 348 347 349 350 CONECT 349 348 354 CONECT 350 348 351 352 CONECT 351 350 364 CONECT 352 350 353 354 CONECT 353 352 CONECT 354 349 352 355 CONECT 355 354 356 362 CONECT 356 355 357 358 CONECT 357 356 CONECT 358 356 359 CONECT 359 358 360 361 CONECT 360 359 CONECT 361 359 362 363 CONECT 362 355 361 CONECT 363 361 CONECT 364 351 CONECT 437 473 CONECT 452 454 462 468 CONECT 453 462 464 465 CONECT 454 452 455 463 CONECT 455 454 457 466 CONECT 456 458 464 467 CONECT 457 455 459 468 CONECT 458 456 460 CONECT 459 457 469 CONECT 460 458 462 CONECT 461 463 470 CONECT 462 452 453 460 CONECT 463 454 461 CONECT 464 453 456 CONECT 465 453 CONECT 466 455 474 CONECT 467 456 CONECT 468 452 457 CONECT 469 459 473 CONECT 470 461 CONECT 471 473 CONECT 472 473 CONECT 473 437 469 471 472 CONECT 474 466 CONECT 515 516 CONECT 516 515 517 CONECT 517 516 518 CONECT 518 517 519 CONECT 519 518 520 CONECT 520 519 521 CONECT 521 520 522 CONECT 522 521 MASTER 214 0 5 0 0 0 0 6 690 2 102 2 END