HEADER RNA 17-MAR-21 7EDT TITLE RNA DUPLEX CONTAINING CC MISPAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*AP*CP*UP*CP*CP*GP*GP*(5BU)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 MISMATCH, BASE PAIR, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,Y.TADA REVDAT 2 03-APR-24 7EDT 1 REMARK REVDAT 1 23-MAR-22 7EDT 0 JRNL AUTH J.KONDO,Y.TADA JRNL TITL RNA DUPLEX CONTAINING CC MISPAIRS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 17949 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.250 REMARK 3 FREE R VALUE TEST SET COUNT : 1840 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 19.2700 - 2.8200 0.87 1152 130 0.1478 0.1760 REMARK 3 2 2.8200 - 2.2400 0.97 1296 131 0.1611 0.1922 REMARK 3 3 2.2400 - 1.9600 0.95 1268 140 0.1408 0.1644 REMARK 3 4 1.9600 - 1.7800 0.95 1235 156 0.1391 0.1771 REMARK 3 5 1.7800 - 1.6500 0.96 1268 158 0.1220 0.1473 REMARK 3 6 1.6500 - 1.5500 0.95 1257 127 0.1270 0.1676 REMARK 3 7 1.5500 - 1.4700 0.94 1264 138 0.1411 0.1849 REMARK 3 8 1.4700 - 1.4100 0.95 1234 150 0.1444 0.1797 REMARK 3 9 1.4100 - 1.3600 0.93 1228 133 0.1429 0.1739 REMARK 3 10 1.3600 - 1.3100 0.94 1255 137 0.1372 0.1862 REMARK 3 11 1.3100 - 1.2700 0.93 1219 145 0.1576 0.2101 REMARK 3 12 1.2700 - 1.2300 0.92 1215 142 0.1416 0.1970 REMARK 3 13 1.2300 - 1.2000 0.92 1218 153 0.1549 0.1953 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) : 15.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.92 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 7EDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-14 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 : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9204 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.4SSI REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17973 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 19.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 3.850 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.75 REMARK 200 R MERGE FOR SHELL (I) : 0.26100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 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: RNA DUPLEX CONSTRUCTED USING COOT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, MPD, 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: 2930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 401 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 6 O2' REMARK 620 2 C A 7 OP2 94.2 REMARK 620 3 G A 8 O6 90.4 167.7 REMARK 620 4 HOH A 537 O 171.0 94.7 81.2 REMARK 620 5 HOH B 134 O 80.5 105.0 87.0 95.6 REMARK 620 N 1 2 3 4 DBREF 7EDT A 1 12 PDB 7EDT 7EDT 1 12 DBREF 7EDT B 13 24 PDB 7EDT 7EDT 13 24 SEQRES 1 A 12 G G A C U C C G G 5BU C C SEQRES 1 B 12 G G A C U C C G G 5BU C C HET 5BU A 10 21 HET 5BU B 22 21 HET SPM A 401 11 HET NA A 402 1 HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE HETNAM SPM SPERMINE HETNAM NA SODIUM ION FORMUL 1 5BU 2(C9 H12 BR N2 O9 P) FORMUL 3 SPM C10 H26 N4 FORMUL 4 NA NA 1+ FORMUL 5 HOH *163(H2 O) LINK O3' G A 9 P 5BU A 10 1555 1555 1.61 LINK O3' 5BU A 10 P C A 11 1555 1555 1.60 LINK O3' G B 21 P 5BU B 22 1555 1555 1.60 LINK O3' 5BU B 22 P C B 23 1555 1555 1.61 LINK O2' C A 6 NA NA A 402 1555 1555 2.50 LINK OP2 C A 7 NA NA A 402 1555 1555 2.33 LINK O6 G A 8 NA NA A 402 1555 1555 2.49 LINK NA NA A 402 O HOH A 537 1555 1555 2.39 LINK NA NA A 402 O HOH B 134 1555 1555 2.43 CRYST1 24.296 24.852 28.249 93.85 106.02 103.21 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 0.041159 0.009663 0.013291 0.00000 SCALE2 0.000000 0.041333 0.005811 0.00000 SCALE3 0.000000 0.000000 0.037192 0.00000 CONECT 116 518 CONECT 128 518 CONECT 163 518 CONECT 177 192 CONECT 192 177 193 194 195 CONECT 193 192 CONECT 194 192 CONECT 195 192 196 CONECT 196 195 197 CONECT 197 196 198 199 CONECT 198 197 203 CONECT 199 197 200 201 CONECT 200 199 213 CONECT 201 199 202 203 CONECT 202 201 CONECT 203 198 201 204 CONECT 204 203 205 211 CONECT 205 204 206 207 CONECT 206 205 CONECT 207 205 208 CONECT 208 207 209 210 CONECT 209 208 CONECT 210 208 211 212 CONECT 211 204 210 CONECT 212 210 CONECT 213 200 CONECT 430 445 CONECT 445 430 446 447 448 CONECT 446 445 CONECT 447 445 CONECT 448 445 449 CONECT 449 448 450 CONECT 450 449 451 452 CONECT 451 450 456 CONECT 452 450 453 454 CONECT 453 452 466 CONECT 454 452 455 456 CONECT 455 454 CONECT 456 451 454 457 CONECT 457 456 458 464 CONECT 458 457 459 460 CONECT 459 458 CONECT 460 458 461 CONECT 461 460 462 463 CONECT 462 461 CONECT 463 461 464 465 CONECT 464 457 463 CONECT 465 463 CONECT 466 453 CONECT 507 508 CONECT 508 507 509 CONECT 509 508 510 CONECT 510 509 511 CONECT 511 510 512 CONECT 512 511 513 CONECT 513 512 514 CONECT 514 513 515 CONECT 515 514 516 CONECT 516 515 517 CONECT 517 516 CONECT 518 116 128 163 555 CONECT 518 629 CONECT 555 518 CONECT 629 518 MASTER 214 0 4 0 0 0 0 6 679 2 64 2 END