HEADER RNA 04-APR-18 6CY2 TITLE RNA OCTAMER CONTAINING 2'-OME, 4'CALPHA-OME U. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOA)P*UP*CP*G)-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 RNA, OLIGONUCLEOTIDE, MODIFIED BASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.HARP,M.EGLI REVDAT 3 13-MAR-24 6CY2 1 REMARK REVDAT 2 03-OCT-18 6CY2 1 JRNL ATOM REVDAT 1 29-AUG-18 6CY2 0 JRNL AUTH J.M.HARP,D.C.GUENTHER,A.BISBE,L.PERKINS,S.MATSUDA, JRNL AUTH 2 G.R.BOMMINENI,I.ZLATEV,D.J.FOSTER,N.TANEJA,K.CHARISSE, JRNL AUTH 3 M.A.MAIER,K.G.RAJEEV,M.MANOHARAN,M.EGLI JRNL TITL STRUCTURAL BASIS FOR THE SYNERGY OF 4'- AND 2'-MODIFICATIONS JRNL TITL 2 ON SIRNA NUCLEASE RESISTANCE, THERMAL STABILITY AND RNAI JRNL TITL 3 ACTIVITY. JRNL REF NUCLEIC ACIDS RES. V. 46 8090 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 30107495 JRNL DOI 10.1093/NAR/GKY703 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2992 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.940 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 16009 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.530 REMARK 3 FREE R VALUE TEST SET COUNT : 726 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 21.4025 - 2.3931 0.99 3060 152 0.1804 0.1905 REMARK 3 2 2.3931 - 1.8999 1.00 3090 143 0.1991 0.2304 REMARK 3 3 1.8999 - 1.6598 0.99 3022 169 0.1490 0.1891 REMARK 3 4 1.6598 - 1.5081 0.98 3089 112 0.1821 0.2390 REMARK 3 5 1.5081 - 1.4000 0.98 3022 150 0.2496 0.3035 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.59 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 6CY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233660. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16014 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 21.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 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) : 1.45 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: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MM RNA; 40 MM SODIUM CACODYLATE, 80 REMARK 280 MM POTASSIUM CHLORIDE, 20 MM MAGNESIUM CHLORIDE, 12 MM SPERMINE. REMARK 280 RESERVOIR 40% MPD, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.80000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 15.75000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 15.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.20000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 15.75000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 15.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.40000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 15.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.75000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 64.20000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 15.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.75000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.40000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.80000 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: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 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: 5VR4 RELATED DB: PDB REMARK 900 5VR4 CONTAINS THE SAME RNA OCTAMER WITH A DIFFERENT 4'-MODIFIED BASE DBREF 6CY2 A 1 8 PDB 6CY2 6CY2 1 8 DBREF 6CY2 B 1 8 PDB 6CY2 6CY2 1 8 SEQRES 1 A 8 CBV G A A UOA U C G SEQRES 1 B 8 CBV G A A UOA U C G HET CBV A 1 27 HET UOA A 5 37 HET CBV B 1 27 HET UOA B 5 37 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM UOA [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)- HETNAM 2 UOA YL)-3-HYDROXY-2,4-DIMETHOXYTETRAHYDROFURAN-2-YL]METHYL HETNAM 3 UOA DIHYDROGEN PHOSPHATE (NON-PREFERRED NAME) FORMUL 1 CBV 2(C9 H13 BR N3 O8 P) FORMUL 1 UOA 2(C11 H17 N2 O10 P) FORMUL 3 HOH *61(H2 O) LINK O3' CBV A 1 P G A 2 1555 1555 1.59 LINK O3' A A 4 P UOA A 5 1555 1555 1.61 LINK O3' UOA A 5 P U A 6 1555 1555 1.60 LINK O3' CBV B 1 P G B 2 1555 1555 1.59 LINK O3' A B 4 P UOA B 5 1555 1555 1.61 LINK O3' UOA B 5 P U B 6 1555 1555 1.61 CRYST1 31.500 31.500 85.600 90.00 90.00 90.00 P 43 21 2 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 0.031746 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011682 0.00000 HETATM 1 O5' CBV A 1 22.834 3.918 -0.357 1.00 30.06 O ANISOU 1 O5' CBV A 1 3268 3901 4252 -374 147 -754 O HETATM 2 C5' CBV A 1 24.152 3.913 0.120 1.00 31.60 C ANISOU 2 C5' CBV A 1 3549 4225 4234 -523 170 -710 C HETATM 3 C4' CBV A 1 24.435 2.509 0.698 1.00 31.47 C ANISOU 3 C4' CBV A 1 3356 4490 4109 -816 166 -864 C HETATM 4 O4' CBV A 1 23.560 2.210 1.824 1.00 31.78 O ANISOU 4 O4' CBV A 1 3485 4669 3920 -731 95 -1087 O HETATM 5 C3' CBV A 1 24.209 1.304 -0.220 1.00 30.63 C ANISOU 5 C3' CBV A 1 3168 4346 4124 -871 152 -1049 C HETATM 6 O3' CBV A 1 25.208 1.149 -1.185 1.00 30.74 O ANISOU 6 O3' CBV A 1 3592 3854 4232 -674 454 -834 O HETATM 7 C2' CBV A 1 24.113 0.159 0.768 1.00 31.38 C ANISOU 7 C2' CBV A 1 3091 4771 4060 -795 -44 -1313 C HETATM 8 O2' CBV A 1 25.401 -0.143 1.287 1.00 33.47 O ANISOU 8 O2' CBV A 1 3337 5154 4226 -237 31 -1387 O HETATM 9 C1' CBV A 1 23.308 0.820 1.879 1.00 32.51 C ANISOU 9 C1' CBV A 1 3510 5001 3843 -746 56 -1218 C HETATM 10 N1 CBV A 1 21.855 0.653 1.694 1.00 31.50 N ANISOU 10 N1 CBV A 1 3624 4811 3534 -691 145 -1342 N HETATM 11 C2 CBV A 1 21.316 -0.497 2.086 1.00 31.98 C ANISOU 11 C2 CBV A 1 3575 5298 3278 -610 191 -1243 C HETATM 12 O2 CBV A 1 22.009 -1.394 2.548 1.00 33.48 O ANISOU 12 O2 CBV A 1 3795 5712 3215 -921 82 -1179 O HETATM 13 N3 CBV A 1 19.975 -0.681 1.947 1.00 30.29 N ANISOU 13 N3 CBV A 1 3188 5235 3087 -382 307 -1240 N HETATM 14 C4 CBV A 1 19.210 0.322 1.440 1.00 30.00 C ANISOU 14 C4 CBV A 1 3195 5139 3065 -208 372 -1386 C HETATM 15 N4 CBV A 1 17.918 0.138 1.316 1.00 29.78 N ANISOU 15 N4 CBV A 1 3115 5294 2906 -462 476 -1386 N HETATM 16 C5 CBV A 1 19.739 1.531 1.039 1.00 29.05 C ANISOU 16 C5 CBV A 1 3194 4510 3334 -385 336 -1558 C HETATM 17 C6 CBV A 1 21.104 1.713 1.158 1.00 31.51 C ANISOU 17 C6 CBV A 1 3934 4589 3451 -422 220 -1621 C HETATM 18 BR CBV A 1 18.632 2.812 0.325 0.69 31.05 BR ANISOU 18 BR CBV A 1 3440 4662 3696 -495 464 -1053 BR HETATM 19 H5'1 CBV A 1 24.843 4.125 -0.696 1.00 37.93 H HETATM 20 H5'2 CBV A 1 24.267 4.666 0.899 1.00 37.93 H HETATM 21 H4' CBV A 1 25.472 2.521 1.035 1.00 37.76 H HETATM 22 H3' CBV A 1 23.251 1.413 -0.729 1.00 36.76 H HETATM 23 H2' CBV A 1 23.615 -0.717 0.351 1.00 37.66 H HETATM 24 HO2' CBV A 1 25.727 0.625 1.838 1.00 40.17 H HETATM 25 H1' CBV A 1 23.624 0.401 2.834 1.00 39.02 H HETATM 26 HN41 CBV A 1 17.343 0.865 0.940 1.00 35.74 H HETATM 27 HN42 CBV A 1 17.507 -0.729 1.599 1.00 35.74 H