HEADER RNA 11-MAR-24 8YNP TITLE RNA DUPLEX CONTAINING METHYLFORMAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHX)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 METHYLFORMAMIDE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,H.ABE REVDAT 1 22-JAN-25 8YNP 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 12149 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1216 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 25.1500 - 2.9100 0.96 1241 139 0.1325 0.1404 REMARK 3 2 2.9000 - 2.3100 0.97 1244 138 0.1769 0.2017 REMARK 3 3 2.3100 - 2.0100 0.95 1227 137 0.1600 0.1889 REMARK 3 4 2.0100 - 1.8300 0.96 1230 137 0.1508 0.1698 REMARK 3 5 1.8300 - 1.7000 0.95 1222 136 0.1453 0.1533 REMARK 3 6 1.7000 - 1.6000 0.93 1194 132 0.1427 0.1805 REMARK 3 7 1.6000 - 1.5200 0.94 1207 134 0.1569 0.2081 REMARK 3 8 1.5200 - 1.4500 0.94 1233 137 0.1667 0.1974 REMARK 3 9 1.4500 - 1.4000 0.90 1135 126 0.1757 0.2106 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.85 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 8YNP 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_1300046012. 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 : 12164 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 25.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 3.576 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.71 REMARK 200 R MERGE FOR SHELL (I) : 0.23100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.070 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 (%): 45.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM CACODYLATE, SPERMINE REMARK 280 TETRAHYDROCHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 2310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8YNO RELATED DB: PDB DBREF 8YNP A 1 12 PDB 8YNP 8YNP 1 12 DBREF 8YNP B 1 12 PDB 8YNP 8YNP 1 12 SEQRES 1 A 12 G G A C 5BU C G A G HHX C C SEQRES 1 B 12 G G A C 5BU C G A G HHX C C HET 5BU A 5 21 HET HHX A 10 23 HET 5BU B 5 21 HET HHX B 10 23 HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE HETNAM HHX [(2R,3S,4R,5R)-5-[2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1- HETNAM 2 HHX YL]-4-[METHANOYL(METHYL)AMINO]-3-OXIDANYL-OXOLAN-2- HETNAM 3 HHX YL]METHYL DIHYDROGEN PHOSPHATE FORMUL 1 5BU 2(C9 H12 BR N2 O9 P) FORMUL 1 HHX 2(C11 H16 N3 O9 P) FORMUL 3 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 1.61 LINK O3' G A 9 P HHX A 10 1555 1555 1.61 LINK O3' HHX A 10 P C A 11 1555 1555 1.59 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 HHX B 10 1555 1555 1.60 LINK O3' HHX B 10 P C B 11 1555 1555 1.60 CRYST1 25.604 27.932 28.668 110.03 114.81 95.76 P 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 0.039056 0.003940 0.021804 0.00000 SCALE2 0.000000 0.035983 0.016932 0.00000 SCALE3 0.000000 0.000000 0.042469 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 180 217 CONECT 195 197 206 212 CONECT 196 206 208 209 CONECT 197 195 198 207 CONECT 198 197 200 210 CONECT 199 201 208 211 CONECT 200 198 202 212 CONECT 201 199 203 CONECT 202 200 213 CONECT 203 201 206 CONECT 204 207 CONECT 205 207 214 CONECT 206 195 196 203 CONECT 207 197 204 205 CONECT 208 196 199 CONECT 209 196 CONECT 210 198 218 CONECT 211 199 CONECT 212 195 200 CONECT 213 202 217 CONECT 214 205 CONECT 215 217 CONECT 216 217 CONECT 217 180 213 215 216 CONECT 218 210 CONECT 332 344 CONECT 344 332 345 346 347 CONECT 345 344 CONECT 346 344 CONECT 347 344 348 CONECT 348 347 349 CONECT 349 348 350 351 CONECT 350 349 355 CONECT 351 349 352 353 CONECT 352 351 365 CONECT 353 351 354 355 CONECT 354 353 CONECT 355 350 353 356 CONECT 356 355 357 363 CONECT 357 356 358 359 CONECT 358 357 CONECT 359 357 360 CONECT 360 359 361 362 CONECT 361 360 CONECT 362 360 363 364 CONECT 363 356 362 CONECT 364 362 CONECT 365 352 CONECT 438 475 CONECT 453 455 464 470 CONECT 454 464 466 467 CONECT 455 453 456 465 CONECT 456 455 458 468 CONECT 457 459 466 469 CONECT 458 456 460 470 CONECT 459 457 461 CONECT 460 458 471 CONECT 461 459 464 CONECT 462 465 CONECT 463 465 472 CONECT 464 453 454 461 CONECT 465 455 462 463 CONECT 466 454 457 CONECT 467 454 CONECT 468 456 476 CONECT 469 457 CONECT 470 453 458 CONECT 471 460 475 CONECT 472 463 CONECT 473 475 CONECT 474 475 CONECT 475 438 471 473 474 CONECT 476 468 MASTER 192 0 4 0 0 0 0 6 684 2 96 2 END