HEADER RNA 12-MAY-20 6WY3 TITLE CRYSTAL STRUCTURE OF RNA-10MER: CCGG(N4,N4-DIMETHYL-C)GCCGG; P212121 TITLE 2 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*CP*GP*GP*(LV2)P*GP*CP*CP*GP*G)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA DUPLEX, RNA EXPDTA X-RAY DIFFRACTION AUTHOR B.SEKULA,M.RUSZKOWSKI,S.MAO,P.HARUEHANROENGRA,J.SHENG REVDAT 3 18-OCT-23 6WY3 1 REMARK REVDAT 2 17-MAR-21 6WY3 1 JRNL REVDAT 1 02-SEP-20 6WY3 0 JRNL AUTH S.MAO,B.SEKULA,M.RUSZKOWSKI,S.V.RANGANATHAN, JRNL AUTH 2 P.HARUEHANROENGRA,Y.WU,F.SHEN,J.SHENG JRNL TITL BASE PAIRING, STRUCTURAL AND FUNCTIONAL INSIGHTS INTO JRNL TITL 2 N4-METHYLCYTIDINE (M4C) AND N4,N4-DIMETHYLCYTIDINE (M42C) JRNL TITL 3 MODIFIED RNA. JRNL REF NUCLEIC ACIDS RES. V. 48 10087 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32941619 JRNL DOI 10.1093/NAR/GKAA737 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 14277 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 692 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 27.9990 - 2.8147 0.93 2968 151 0.1622 0.1893 REMARK 3 2 2.8147 - 2.2344 0.93 2803 147 0.2228 0.2354 REMARK 3 3 2.2344 - 1.9520 0.98 2942 144 0.2137 0.2456 REMARK 3 4 1.9520 - 1.7736 0.93 2766 146 0.2147 0.2410 REMARK 3 5 1.7736 - 1.6465 0.71 2106 104 0.2232 0.2556 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 952 REMARK 3 ANGLE : 1.158 1480 REMARK 3 CHIRALITY : 0.042 192 REMARK 3 PLANARITY : 0.006 44 REMARK 3 DIHEDRAL : 9.551 468 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.1403 18.5122 50.7379 REMARK 3 T TENSOR REMARK 3 T11: 0.2856 T22: 0.1803 REMARK 3 T33: 0.1798 T12: 0.0048 REMARK 3 T13: 0.0108 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 3.0886 L22: 0.3893 REMARK 3 L33: 0.8517 L12: -1.0618 REMARK 3 L13: -2.0477 L23: 0.8825 REMARK 3 S TENSOR REMARK 3 S11: 0.0508 S12: -0.1549 S13: 0.1528 REMARK 3 S21: 0.0534 S22: 0.0706 S23: 0.0376 REMARK 3 S31: -0.0530 S32: 0.0862 S33: -0.1307 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.9602 18.2295 46.1783 REMARK 3 T TENSOR REMARK 3 T11: 0.2203 T22: 0.1765 REMARK 3 T33: 0.1292 T12: -0.0136 REMARK 3 T13: -0.0103 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 2.9348 L22: 2.2812 REMARK 3 L33: 1.0291 L12: -0.7190 REMARK 3 L13: -1.8061 L23: 0.1417 REMARK 3 S TENSOR REMARK 3 S11: -0.0021 S12: 0.2733 S13: 0.0927 REMARK 3 S21: -0.0959 S22: 0.0422 S23: -0.1065 REMARK 3 S31: 0.1453 S32: -0.1118 S33: -0.0821 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7057 17.1413 23.5437 REMARK 3 T TENSOR REMARK 3 T11: 0.2230 T22: 0.2583 REMARK 3 T33: 0.1670 T12: -0.0276 REMARK 3 T13: -0.0102 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 0.4398 L22: 2.3649 REMARK 3 L33: 1.7234 L12: 0.9406 REMARK 3 L13: -1.6451 L23: -2.9190 REMARK 3 S TENSOR REMARK 3 S11: 0.1532 S12: -0.1082 S13: 0.0301 REMARK 3 S21: 0.1808 S22: 0.0559 S23: 0.2271 REMARK 3 S31: -0.0489 S32: 0.0422 S33: -0.1961 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8540 15.6729 19.6610 REMARK 3 T TENSOR REMARK 3 T11: 0.2410 T22: 0.1994 REMARK 3 T33: 0.1200 T12: 0.0347 REMARK 3 T13: -0.0149 T23: -0.0476 REMARK 3 L TENSOR REMARK 3 L11: 1.3522 L22: 3.1406 REMARK 3 L33: 3.1197 L12: -0.3103 REMARK 3 L13: 0.4966 L23: -3.8810 REMARK 3 S TENSOR REMARK 3 S11: 0.1291 S12: 0.0724 S13: 0.0230 REMARK 3 S21: -0.3498 S22: 0.0035 S23: 0.1188 REMARK 3 S31: 0.2745 S32: 0.0785 S33: -0.0949 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 6WY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000240689. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14279 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.647 REMARK 200 RESOLUTION RANGE LOW (A) : 27.995 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.67700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 4MS9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V/V (+/-)-2-METHYL-2,4-PENTANEDIOL REMARK 280 (MPD), 0.040 M SODIUM CACODYLATE TRIHYDRATE PH 7.0, 0.012 M REMARK 280 SPERMINE TETRAHYDROCHLORIDE, 0.08M SODIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 16.54300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.52500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.09200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.52500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.54300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.09200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 DBREF 6WY3 A 1 10 PDB 6WY3 6WY3 1 10 DBREF 6WY3 B 1 10 PDB 6WY3 6WY3 1 10 DBREF 6WY3 C 1 10 PDB 6WY3 6WY3 1 10 DBREF 6WY3 D 1 10 PDB 6WY3 6WY3 1 10 SEQRES 1 A 10 C C G G LV2 G C C G G SEQRES 1 B 10 C C G G LV2 G C C G G SEQRES 1 C 10 C C G G LV2 G C C G G SEQRES 1 D 10 C C G G LV2 G C C G G HET LV2 A 5 22 HET LV2 B 5 22 HET LV2 C 5 22 HET LV2 D 5 22 HETNAM LV2 [(2~{R},3~{S},4~{R},5~{R})-5-[4-(DIMETHYLAMINO)-2- HETNAM 2 LV2 OXIDANYLIDENE-PYRIMIDIN-1-YL]-3,4-BIS(OXIDANYL)OXOLAN- HETNAM 3 LV2 2-YL]METHYL DIHYDROGEN PHOSPHATE FORMUL 1 LV2 4(C11 H18 N3 O8 P) FORMUL 5 HOH *187(H2 O) LINK O3' G A 4 P LV2 A 5 1555 1555 1.60 LINK O3' LV2 A 5 P G A 6 1555 1555 1.60 LINK O3' G B 4 P LV2 B 5 1555 1555 1.60 LINK O3' LV2 B 5 P G B 6 1555 1555 1.60 LINK O3' G C 4 P LV2 C 5 1555 1555 1.60 LINK O3' LV2 C 5 P G C 6 1555 1555 1.60 LINK O3' G D 4 P LV2 D 5 1555 1555 1.61 LINK O3' LV2 D 5 P G D 6 1555 1555 1.59 CRYST1 33.086 36.184 105.050 90.00 90.00 90.00 P 21 21 21 16 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 0.030224 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027637 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009519 0.00000 CONECT 69 84 CONECT 84 69 85 86 87 CONECT 85 84 CONECT 86 84 CONECT 87 84 88 CONECT 88 87 89 CONECT 89 88 90 91 CONECT 90 89 94 CONECT 91 89 92 104 CONECT 92 91 93 94 CONECT 93 92 CONECT 94 90 92 95 CONECT 95 94 96 102 CONECT 96 95 97 98 CONECT 97 96 CONECT 98 96 99 CONECT 99 98 100 101 CONECT 100 99 103 105 CONECT 101 99 102 CONECT 102 95 101 CONECT 103 100 CONECT 104 91 106 CONECT 105 100 CONECT 106 104 CONECT 284 299 CONECT 299 284 300 301 302 CONECT 300 299 CONECT 301 299 CONECT 302 299 303 CONECT 303 302 304 CONECT 304 303 305 306 CONECT 305 304 309 CONECT 306 304 307 319 CONECT 307 306 308 309 CONECT 308 307 CONECT 309 305 307 310 CONECT 310 309 311 317 CONECT 311 310 312 313 CONECT 312 311 CONECT 313 311 314 CONECT 314 313 315 316 CONECT 315 314 318 320 CONECT 316 314 317 CONECT 317 310 316 CONECT 318 315 CONECT 319 306 321 CONECT 320 315 CONECT 321 319 CONECT 499 514 CONECT 514 499 515 516 517 CONECT 515 514 CONECT 516 514 CONECT 517 514 518 CONECT 518 517 519 CONECT 519 518 520 521 CONECT 520 519 524 CONECT 521 519 522 534 CONECT 522 521 523 524 CONECT 523 522 CONECT 524 520 522 525 CONECT 525 524 526 532 CONECT 526 525 527 528 CONECT 527 526 CONECT 528 526 529 CONECT 529 528 530 531 CONECT 530 529 533 535 CONECT 531 529 532 CONECT 532 525 531 CONECT 533 530 CONECT 534 521 536 CONECT 535 530 CONECT 536 534 CONECT 714 729 CONECT 729 714 730 731 732 CONECT 730 729 CONECT 731 729 CONECT 732 729 733 CONECT 733 732 734 CONECT 734 733 735 736 CONECT 735 734 739 CONECT 736 734 737 749 CONECT 737 736 738 739 CONECT 738 737 CONECT 739 735 737 740 CONECT 740 739 741 747 CONECT 741 740 742 743 CONECT 742 741 CONECT 743 741 744 CONECT 744 743 745 746 CONECT 745 744 748 750 CONECT 746 744 747 CONECT 747 740 746 CONECT 748 745 CONECT 749 736 751 CONECT 750 745 CONECT 751 749 MASTER 270 0 4 0 0 0 0 6 1043 4 96 4 END