HEADER RNA 04-APR-18 6CY0 TITLE RNA OCTAMER CONTAINING 2'-F, 4'-CBETA-OME U. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3'); COMPND 3 CHAIN: A, B, C, D, E, F, G, H; 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 6CY0 1 REMARK REVDAT 2 03-OCT-18 6CY0 1 JRNL REVDAT 1 29-AUG-18 6CY0 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 16693 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 855 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 42.6088 - 4.3557 0.97 2652 120 0.1700 0.2236 REMARK 3 2 4.3557 - 3.4578 0.99 2662 154 0.1794 0.2034 REMARK 3 3 3.4578 - 3.0208 0.97 2604 155 0.1896 0.2493 REMARK 3 4 3.0208 - 2.7447 1.00 2739 119 0.2478 0.2550 REMARK 3 5 2.7447 - 2.5480 0.98 2672 132 0.2391 0.2852 REMARK 3 6 2.5480 - 2.3978 0.95 2509 175 0.2381 0.2835 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.78 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 6CY0 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_1000233659. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 0.9184 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 : 9164 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.398 REMARK 200 RESOLUTION RANGE LOW (A) : 42.602 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 21.60 REMARK 200 R MERGE (I) : 0.19800 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43300 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 (%): 60.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 MM RNA; 100 MM MES, 2.5 M AMMONIUM REMARK 280 SULFATE, 10 MM MAGNESIUM CHLORIDE,, PH 5.6, VAPOR DIFFUSION, REMARK 280 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 23.50600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.37200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.81550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.37200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.50600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.81550 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, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC 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 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 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 G 119 DISTANCE = 6.12 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VR4 RELATED DB: PDB REMARK 900 5VR4 CONTAINS THE SAME RNA OCTAMER WITH A DIFFERNT 4'-MODIFIED BASE. DBREF 6CY0 A 1 8 PDB 6CY0 6CY0 1 8 DBREF 6CY0 B 1 8 PDB 6CY0 6CY0 1 8 DBREF 6CY0 C 1 8 PDB 6CY0 6CY0 1 8 DBREF 6CY0 D 1 8 PDB 6CY0 6CY0 1 8 DBREF 6CY0 E 1 8 PDB 6CY0 6CY0 1 8 DBREF 6CY0 F 1 8 PDB 6CY0 6CY0 1 8 DBREF 6CY0 G 1 8 PDB 6CY0 6CY0 1 8 DBREF 6CY0 H 1 8 PDB 6CY0 6CY0 1 8 SEQRES 1 A 8 CBV G A A UFB U C G SEQRES 1 B 8 CBV G A A UFB U C G SEQRES 1 C 8 CBV G A A UFB U C G SEQRES 1 D 8 CBV G A A UFB U C G SEQRES 1 E 8 CBV G A A UFB U C G SEQRES 1 F 8 CBV G A A UFB U C G SEQRES 1 G 8 CBV G A A UFB U C G SEQRES 1 H 8 CBV G A A UFB U C G HET CBV A 1 27 HET UFB A 5 33 HET CBV B 1 27 HET UFB B 5 33 HET CBV C 1 27 HET UFB C 5 33 HET CBV D 1 27 HET UFB D 5 33 HET CBV E 1 27 HET UFB E 5 33 HET CBV F 1 27 HET UFB F 5 33 HET CBV G 1 27 HET UFB G 5 33 HET CBV H 1 28 HET UFB H 5 33 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM UFB 2'-F,4'-BETA-OME URIDINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 1 CBV 8(C9 H13 BR N3 O8 P) FORMUL 1 UFB 8(C10 H14 F N2 O9 P) FORMUL 9 HOH *175(H2 O) LINK O3' CBV A 1 P G A 2 1555 1555 1.61 LINK O3' A A 4 P UFB A 5 1555 1555 1.61 LINK O3' UFB A 5 P U A 6 1555 1555 1.61 LINK O3' CBV B 1 P G B 2 1555 1555 1.61 LINK O3' A B 4 P UFB B 5 1555 1555 1.61 LINK O3' UFB B 5 P U B 6 1555 1555 1.61 LINK O3' CBV C 1 P G C 2 1555 1555 1.61 LINK O3' A C 4 P UFB C 5 1555 1555 1.62 LINK O3' UFB C 5 P U C 6 1555 1555 1.61 LINK O3' CBV D 1 P G D 2 1555 1555 1.61 LINK O3' A D 4 P UFB D 5 1555 1555 1.61 LINK O3' UFB D 5 P U D 6 1555 1555 1.59 LINK O3' CBV E 1 P G E 2 1555 1555 1.61 LINK O3' A E 4 P UFB E 5 1555 1555 1.61 LINK O3' UFB E 5 P U E 6 1555 1555 1.61 LINK O3' CBV F 1 P G F 2 1555 1555 1.61 LINK O3' A F 4 P UFB F 5 1555 1555 1.61 LINK O3' UFB F 5 P U F 6 1555 1555 1.61 LINK O3' CBV G 1 P G G 2 1555 1555 1.61 LINK O3' A G 4 P UFB G 5 1555 1555 1.61 LINK O3' UFB G 5 P U G 6 1555 1555 1.61 LINK O3' CBV H 1 P G H 2 1555 1555 1.61 LINK O3' A H 4 P UFB H 5 1555 1555 1.61 LINK O3' UFB H 5 P U H 6 1555 1555 1.61 CRYST1 47.012 47.631 100.744 90.00 90.00 90.00 P 21 21 21 32 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 0.021273 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021001 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009927 0.00000 HETATM 1 O5' CBV A 1 7.276 -0.564 -9.095 1.00 17.26 O HETATM 2 C5' CBV A 1 7.919 -1.644 -8.433 1.00 18.59 C HETATM 3 C4' CBV A 1 9.214 -1.207 -7.804 1.00 17.92 C HETATM 4 O4' CBV A 1 9.000 -0.106 -6.881 1.00 10.61 O HETATM 5 C3' CBV A 1 9.946 -2.240 -6.955 1.00 14.75 C HETATM 6 O3' CBV A 1 10.607 -3.215 -7.736 1.00 19.22 O HETATM 7 C2' CBV A 1 10.880 -1.355 -6.146 1.00 15.20 C HETATM 8 O2' CBV A 1 11.934 -0.899 -6.989 1.00 28.90 O HETATM 9 C1' CBV A 1 9.977 -0.152 -5.860 1.00 15.74 C HETATM 10 N1 CBV A 1 9.296 -0.197 -4.540 1.00 11.65 N HETATM 11 C2 CBV A 1 10.026 0.094 -3.452 1.00 11.53 C HETATM 12 O2 CBV A 1 11.227 0.341 -3.556 1.00 6.79 O HETATM 13 N3 CBV A 1 9.444 0.105 -2.189 1.00 14.80 N HETATM 14 C4 CBV A 1 8.093 -0.163 -2.031 1.00 9.10 C HETATM 15 N4 CBV A 1 7.514 -0.159 -0.828 1.00 12.96 N HETATM 16 C5 CBV A 1 7.313 -0.452 -3.144 1.00 12.40 C HETATM 17 C6 CBV A 1 7.919 -0.461 -4.403 1.00 10.07 C HETATM 18 BR CBV A 1 5.478 -0.823 -2.957 0.41 13.21 BR HETATM 19 H5'1 CBV A 1 8.124 -2.432 -9.157 1.00 22.36 H HETATM 20 H5'2 CBV A 1 7.258 -2.027 -7.655 1.00 22.36 H HETATM 21 H4' CBV A 1 9.871 -0.870 -8.606 1.00 21.56 H HETATM 22 H3' CBV A 1 9.249 -2.742 -6.284 1.00 17.75 H HETATM 23 H2' CBV A 1 11.229 -1.836 -5.233 1.00 18.30 H HETATM 24 HO2' CBV A 1 12.558 -0.323 -6.461 1.00 34.74 H HETATM 25 H1' CBV A 1 10.590 0.749 -5.883 1.00 18.94 H HETATM 26 HN41 CBV A 1 8.056 0.046 -0.013 1.00 15.60 H HETATM 27 HN42 CBV A 1 6.539 -0.360 -0.742 1.00 15.60 H