HEADER RNA 14-JAN-22 7QTN TITLE DUPLEX RNA CONTAINING XANTHOSINE-CYTOSINE BASE PAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*UP*AP*(RY)P*UP*GP*CP*GP*(XAN) COMPND 3 P*UP*AP*CP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*GP*GP*UP*AP*CP*UP*GP*CP*GP*(XAM)P*UP*AP*CP*C)- COMPND 8 3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS RNA, MODIFIED BASE EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR,R.MICURA REVDAT 3 31-JAN-24 7QTN 1 REMARK REVDAT 2 23-AUG-23 7QTN 1 JRNL REVDAT 1 25-JAN-23 7QTN 0 JRNL AUTH S.MAIR,K.ERHARTER,E.RENARD,K.BRILLET,M.BRUNNER,A.LUSSER, JRNL AUTH 2 C.KREUTZ,E.ENNIFAR,R.MICURA JRNL TITL TOWARDS A COMPREHENSIVE UNDERSTANDING OF RNA DEAMINATION: JRNL TITL 2 SYNTHESIS AND PROPERTIES OF XANTHOSINE-MODIFIED RNA. JRNL REF NUCLEIC ACIDS RES. V. 50 6038 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35687141 JRNL DOI 10.1093/NAR/GKAC477 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28981 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1449 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 38.8700 - 2.5900 0.99 3031 160 0.1787 0.2021 REMARK 3 2 2.5900 - 2.0500 1.00 2811 148 0.1801 0.2018 REMARK 3 3 2.0500 - 1.7900 1.00 2779 146 0.1506 0.1645 REMARK 3 4 1.7900 - 1.6300 0.99 2725 144 0.1376 0.1792 REMARK 3 5 1.6300 - 1.5100 1.00 2724 142 0.1612 0.2158 REMARK 3 6 1.5100 - 1.4200 1.00 2715 143 0.1975 0.2352 REMARK 3 7 1.4200 - 1.3500 1.00 2696 142 0.2380 0.2850 REMARK 3 8 1.3500 - 1.2900 1.00 2684 142 0.2804 0.3334 REMARK 3 9 1.2900 - 1.2400 1.00 2680 141 0.3496 0.3530 REMARK 3 10 1.2400 - 1.2000 1.00 2687 141 0.3760 0.4197 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.50 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.227 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.41 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 : 0.008 660 REMARK 3 ANGLE : 1.099 1026 REMARK 3 CHIRALITY : 0.045 135 REMARK 3 PLANARITY : 0.013 28 REMARK 3 DIHEDRAL : 6.751 303 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 7QTN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-21 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1894942 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.3000 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) : 1.23 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: MOLREP REMARK 200 STARTING MODEL: 433D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM SULFATE, TRIS HCL, AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.85000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 74.85000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 74.85000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 74.85000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 74.85000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 74.85000 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 119 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 120 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 125 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 140 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 141 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 148 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 149 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 131 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 134 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 159 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 166 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 167 LIES ON A SPECIAL POSITION. 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 168 DISTANCE = 5.95 ANGSTROMS DBREF 7QTN A 1 14 PDB 7QTN 7QTN 1 14 DBREF 7QTN B 15 28 PDB 7QTN 7QTN 15 28 SEQRES 1 A 14 G G U A RY U G C G HYJ U A C SEQRES 2 A 14 C SEQRES 1 B 14 G G U A C U G C G XMP U A C SEQRES 2 B 14 C HET RY A 5 32 HET HYJ A 10 33 HET XMP B 24 32 HETNAM RY 5'-3,6-DIHYDROCYTIDYLIC ACID HETNAM HYJ 9-[(2~{R},3~{R},4~{S},5~{R})-3,4-BIS(OXIDANYL)-5- HETNAM 2 HYJ [[TRIS(OXIDANYL)-$L^{5}-PHOSPHANYL]OXYMETHYL]OXOLAN-2- HETNAM 3 HYJ YL]-2-OXIDANYL-1~{H}-PURIN-6-ONE HETNAM XMP XANTHOSINE-5'-MONOPHOSPHATE HETSYN XMP 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE FORMUL 1 RY C9 H16 N3 O8 P FORMUL 1 HYJ C10 H13 N4 O9 P FORMUL 2 XMP C10 H14 N4 O9 P 1+ FORMUL 3 HOH *121(H2 O) LINK O3' A A 4 P RY A 5 1555 1555 1.61 LINK O3' RY A 5 P U A 6 1555 1555 1.61 LINK O3' G A 9 P HYJ A 10 1555 1555 1.61 LINK O3' HYJ A 10 P U A 11 1555 1555 1.62 LINK O3' G B 23 P XMP B 24 1555 1555 1.61 LINK O3' XMP B 24 P U B 25 1555 1555 1.61 CRYST1 44.880 44.880 149.700 90.00 90.00 120.00 P 63 2 2 12 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 0.022282 0.012864 0.000000 0.00000 SCALE2 0.000000 0.025729 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006680 0.00000 CONECT 105 130 CONECT 130 105 132 148 149 CONECT 131 132 133 150 151 CONECT 132 130 131 CONECT 133 131 134 135 152 CONECT 134 133 139 CONECT 135 133 136 137 153 CONECT 136 135 162 CONECT 137 135 138 139 154 CONECT 138 137 155 CONECT 139 134 137 140 156 CONECT 140 139 141 147 CONECT 141 140 142 143 CONECT 142 141 CONECT 143 141 144 157 CONECT 144 143 145 146 CONECT 145 144 158 159 CONECT 146 144 147 160 CONECT 147 140 146 161 CONECT 148 130 CONECT 149 130 CONECT 150 131 CONECT 151 131 CONECT 152 133 CONECT 153 135 CONECT 154 137 CONECT 155 138 CONECT 156 139 CONECT 157 143 CONECT 158 145 CONECT 159 145 CONECT 160 146 CONECT 161 147 CONECT 162 136 CONECT 265 313 CONECT 291 292 301 302 CONECT 292 291 293 299 CONECT 293 292 294 CONECT 294 293 295 296 CONECT 295 294 314 CONECT 296 294 297 315 CONECT 297 296 298 299 CONECT 298 297 CONECT 299 292 297 300 CONECT 300 299 301 CONECT 301 291 300 316 CONECT 302 291 303 309 317 CONECT 303 302 304 307 318 CONECT 304 303 305 308 319 CONECT 305 304 306 309 320 CONECT 306 305 310 321 322 CONECT 307 303 323 CONECT 308 304 324 CONECT 309 302 305 CONECT 310 306 313 CONECT 311 313 CONECT 312 313 CONECT 313 265 310 311 312 CONECT 314 295 CONECT 315 296 CONECT 316 301 CONECT 317 302 CONECT 318 303 CONECT 319 304 CONECT 320 305 CONECT 321 306 CONECT 322 306 CONECT 323 307 CONECT 324 308 CONECT 714 740 CONECT 740 714 741 742 743 CONECT 741 740 CONECT 742 740 CONECT 743 740 744 CONECT 744 743 745 763 764 CONECT 745 744 746 761 765 CONECT 746 745 747 CONECT 747 746 748 759 766 CONECT 748 747 749 758 CONECT 749 748 750 756 CONECT 750 749 752 CONECT 751 752 754 767 CONECT 752 750 751 753 CONECT 753 752 CONECT 754 751 755 756 CONECT 755 754 CONECT 756 749 754 757 CONECT 757 756 758 CONECT 758 748 757 768 CONECT 759 747 760 761 769 CONECT 760 759 770 CONECT 761 745 759 762 771 CONECT 762 761 772 CONECT 763 744 CONECT 764 744 CONECT 765 745 CONECT 766 747 CONECT 767 751 CONECT 768 758 CONECT 769 759 CONECT 770 760 CONECT 771 761 CONECT 772 762 MASTER 260 0 3 0 0 0 0 6 713 2 103 4 END