HEADER RNA 09-FEB-21 7LO9 TITLE RNA DODECAMER CONTAINING A GNA A RESIDUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAINS: A,B,C,D; 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 CRYSTAL STRUCTURE, GLYCOL NUCLEIC ACID, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.M.HARP,Z.WAWRZAK,M.EGLI REVDAT 2 22-MAY-24 7LO9 1 REMARK REVDAT 1 22-DEC-21 7LO9 0 JRNL AUTH M.K.SCHLEGEL,S.MATSUDA,C.R.BROWN,J.M.HARP,J.D.BARRY, JRNL AUTH 2 D.BERMAN,A.CASTORENO,S.SCHOFIELD,J.SZETO,M.MANOHARAN, JRNL AUTH 3 K.CHARISSE,M.EGLI,M.A.MAIER JRNL TITL OVERCOMING GNA/RNA BASE-PAIRING LIMITATIONS USING JRNL TITL 2 ISONUCLEOTIDES IMPROVES THE PHARMACODYNAMIC ACTIVITY OF ESC+ JRNL TITL 3 GALNAC-SIRNAS. JRNL REF NUCLEIC ACIDS RES. V. 49 10851 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 34648028 JRNL DOI 10.1093/NAR/GKAB916 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.940 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 12298 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.530 REMARK 3 FREE R VALUE TEST SET COUNT : 1111 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 23.7600 - 3.5600 1.00 2903 164 0.1080 0.1488 REMARK 3 2 3.5600 - 2.8300 1.00 2962 136 0.1948 0.2488 REMARK 3 3 2.8200 - 2.4700 1.00 2917 108 0.2866 0.3313 REMARK 3 4 2.4700 - 2.2400 1.00 2925 138 0.3247 0.4145 REMARK 3 5 2.2400 - 2.0800 1.00 2880 174 0.3367 0.3290 REMARK 3 6 2.0800 - 1.9600 1.00 2893 152 0.3479 0.3543 REMARK 3 7 1.9600 - 1.8600 0.99 3013 100 0.3627 0.3988 REMARK 3 8 1.8600 - 1.7800 0.98 2937 139 0.3974 0.4084 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) : 0.106 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 47.628 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.75 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 : 0.002 1116 REMARK 3 ANGLE : 0.534 1712 REMARK 3 CHIRALITY : 0.021 212 REMARK 3 PLANARITY : 0.002 48 REMARK 3 DIHEDRAL : 14.834 532 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 7LO9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000254744. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-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 : 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24620 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 26.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 26.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 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: EQUILATERAL TRIANGULAR PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROP CONTAINING 0.5 MM REMARK 280 OLIGONUCLEOTIDE, 2.3 MM HOCL3, 40 MM NACL, 5 MM SPERMINE 4HCL, REMARK 280 20 MM NA CACODYLATE, PH 7.0 EQUILIBRATED AGAINST 40% MPD, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 88.76000 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 44.38000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 G C 4 C3' - O3' - P ANGL. DEV. = -7.8 DEGREES REMARK 500 G D 4 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 7LO9 A 1 12 PDB 7LO9 7LO9 1 12 DBREF 7LO9 B 1 12 PDB 7LO9 7LO9 1 12 DBREF 7LO9 C 1 12 PDB 7LO9 7LO9 1 12 DBREF 7LO9 D 1 12 PDB 7LO9 7LO9 1 12 SEQRES 1 A 12 C G C G ZAD A 5BU U A G C G SEQRES 1 B 12 C G C G ZAD A 5BU U A G C G SEQRES 1 C 12 C G C G ZAD A 5BU U A G C G SEQRES 1 D 12 C G C G ZAD A 5BU U A G C G HET ZAD A 5 26 HET 5BU A 7 30 HET ZAD B 5 26 HET 5BU B 7 30 HET ZAD C 5 26 HET 5BU C 7 30 HET ZAD D 5 26 HET 5BU D 7 30 HETNAM ZAD (S)-1'-(2',3'-DIHYDROXYPROPYL)-ADENINE HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE FORMUL 1 ZAD 4(C8 H12 N5 O5 P) FORMUL 1 5BU 4(C9 H12 BR N2 O9 P) FORMUL 5 HOH *16(H2 O) LINK O3' G A 4 P ZAD A 5 1555 1555 1.56 LINK O2G ZAD A 5 P A A 6 1555 1555 1.56 LINK O3' A A 6 P 5BU A 7 1555 1555 1.61 LINK O3' 5BU A 7 P U A 8 1555 1555 1.61 LINK O3' G B 4 P ZAD B 5 1555 1555 1.56 LINK O2G ZAD B 5 P A B 6 1555 1555 1.56 LINK O3' A B 6 P 5BU B 7 1555 1555 1.60 LINK O3' 5BU B 7 P U B 8 1555 1555 1.61 LINK O3' G C 4 P ZAD C 5 1555 1555 1.56 LINK O2G ZAD C 5 P A C 6 1555 1555 1.56 LINK O3' A C 6 P 5BU C 7 1555 1555 1.61 LINK O3' 5BU C 7 P U C 8 1555 1555 1.61 LINK O3' G D 4 P ZAD D 5 1555 1555 1.56 LINK O2G ZAD D 5 P A D 6 1555 1555 1.56 LINK O3' A D 6 P 5BU D 7 1555 1555 1.61 LINK O3' 5BU D 7 P U D 8 1555 1555 1.61 CRYST1 29.370 29.370 133.140 90.00 90.00 120.00 P 32 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 0.034048 0.019658 0.000000 0.00000 SCALE2 0.000000 0.039316 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007511 0.00000