HEADER RNA 30-JUL-14 4U78 TITLE OCTAMERIC RNA DUPLEX SOAKED IN COPPER(II)CHLORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*UP*CP*GP*UP*AP*CP*GP*A)-3'); COMPND 3 CHAIN: B, A; 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, DIVALENT METAL IONS EXPDTA X-RAY DIFFRACTION AUTHOR M.F.SCHAFFER,B.SPINGLER,J.SCHNABL,G.PENG,V.OLIERIC,R.K.O.SIGEL REVDAT 3 20-DEC-23 4U78 1 LINK REVDAT 2 13-JUL-16 4U78 1 JRNL REVDAT 1 26-AUG-15 4U78 0 JRNL AUTH M.F.SCHAFFER,G.PENG,B.SPINGLER,J.SCHNABL,M.WANG,V.OLIERIC, JRNL AUTH 2 R.K.SIGEL JRNL TITL THE X-RAY STRUCTURES OF SIX OCTAMERIC RNA DUPLEXES IN THE JRNL TITL 2 PRESENCE OF DIFFERENT DI- AND TRIVALENT CATIONS. JRNL REF INT J MOL SCI V. 17 2016 JRNL REFN ESSN 1422-0067 JRNL PMID 27355942 JRNL DOI 10.3390/IJMS17070988 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 6862 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.540 REMARK 3 FREE R VALUE TEST SET COUNT : 723 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 32.2916 - 2.5658 1.00 1254 150 0.1486 0.1724 REMARK 3 2 2.5658 - 2.0367 1.00 1244 137 0.1899 0.2433 REMARK 3 3 2.0367 - 1.7793 1.00 1255 144 0.1981 0.2207 REMARK 3 4 1.7793 - 1.6166 0.99 1235 150 0.1992 0.2256 REMARK 3 5 1.6166 - 1.5007 0.93 1151 142 0.2409 0.3003 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.370 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 : 0.036 397 REMARK 3 ANGLE : 0.403 576 REMARK 3 CHIRALITY : 0.018 78 REMARK 3 PLANARITY : 0.003 16 REMARK 3 DIHEDRAL : 5.082 184 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 4U78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000202930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.37 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6864 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 32.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.03198 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.35010 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 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: 4U3L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 400, 0.2 M CALCIUM CHLORIDE, REMARK 280 0.002 M SPERMINE, 0.05 M HEPES SODIUM BUFFER, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 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 23.40500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.51288 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.79333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 23.40500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 13.51288 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 17.79333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 23.40500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 13.51288 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 17.79333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.02577 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 35.58667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.02577 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 35.58667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.02577 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 35.58667 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: 2950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A 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 CA CA A 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 213 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 216 LIES ON A SPECIAL POSITION. REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 206 O REMARK 620 2 HOH B 208 O 76.7 REMARK 620 3 HOH B 219 O 139.7 78.7 REMARK 620 4 HOH B 220 O 114.5 75.1 88.9 REMARK 620 5 HOH A 217 O 90.7 163.8 117.4 101.7 REMARK 620 6 HOH A 218 O 146.8 122.8 73.5 55.7 64.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 222 O REMARK 620 2 HOH B 223 O 75.6 REMARK 620 3 HOH B 229 O 78.7 101.7 REMARK 620 4 U A 4 O4 146.2 138.1 93.4 REMARK 620 5 HOH A 221 O 132.9 68.1 80.4 76.4 REMARK 620 6 HOH A 222 O 94.0 83.8 169.3 88.3 110.2 REMARK 620 7 HOH A 227 O 76.8 144.1 95.0 71.1 146.9 75.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 222 O REMARK 620 2 HOH B 223 O 74.1 REMARK 620 3 HOH B 229 O 75.7 100.6 REMARK 620 4 U A 4 O4 143.0 142.8 93.4 REMARK 620 5 HOH A 221 O 131.9 69.6 80.9 79.0 REMARK 620 6 HOH A 222 O 92.5 84.9 164.8 90.4 114.2 REMARK 620 7 HOH A 227 O 74.0 141.4 92.2 71.1 148.9 75.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 7 OP1 REMARK 620 2 G A 7 OP1 0.0 REMARK 620 3 HOH A 216 O 84.2 84.2 REMARK 620 4 HOH A 216 O 87.6 87.6 88.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4U3L RELATED DB: PDB REMARK 900 SAME SEQUENCE REMARK 900 RELATED ID: 4U3R RELATED DB: PDB REMARK 900 SAME SEQUENCE REMARK 900 RELATED ID: 4U3O RELATED DB: PDB REMARK 900 SAME SEQUENCE REMARK 900 RELATED ID: 4U3P RELATED DB: PDB REMARK 900 SAME SEQUENCE REMARK 900 RELATED ID: 4U47 RELATED DB: PDB REMARK 900 SAME SEQUENCE DBREF 4U78 B 1 8 PDB 4U78 4U78 1 8 DBREF 4U78 A 1 8 PDB 4U78 4U78 1 8 SEQRES 1 B 8 U C G U A C G A SEQRES 1 A 8 U C G U A C G A HET CU B 101 1 HET CU A 101 1 HET CA A 102 1 HET CA A 103 1 HETNAM CU COPPER (II) ION HETNAM CA CALCIUM ION FORMUL 3 CU 2(CU 2+) FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *78(H2 O) LINK CU CU B 101 O HOH B 206 1555 1555 2.11 LINK CU CU B 101 O HOH B 208 1555 1555 2.27 LINK CU CU B 101 O HOH B 219 1555 1555 2.22 LINK CU CU B 101 O HOH B 220 1555 8444 2.17 LINK CU CU B 101 O HOH A 217 1555 8444 2.21 LINK CU CU B 101 O HOH A 218 1555 8444 2.15 LINK O HOH B 222 CU CU A 101 1555 1555 2.31 LINK O HOH B 222 CA CA A 102 1555 1555 2.40 LINK O HOH B 223 CU CU A 101 1555 1555 2.38 LINK O HOH B 223 CA CA A 102 1555 1555 2.37 LINK O HOH B 229 CU CU A 101 1555 1555 2.30 LINK O HOH B 229 CA CA A 102 1555 1555 2.36 LINK O4 U A 4 CU CU A 101 1555 1555 2.40 LINK O4 U A 4 CA CA A 102 1555 1555 2.35 LINK OP1 G A 7 CA CA A 103 1555 1555 2.35 LINK OP1 G A 7 CA CA A 103 1555 2455 2.35 LINK CU CU A 101 O HOH A 221 1555 1555 2.44 LINK CU CU A 101 O HOH A 222 1555 1555 2.38 LINK CU CU A 101 O HOH A 227 1555 1555 2.32 LINK CA CA A 102 O HOH A 221 1555 1555 2.37 LINK CA CA A 102 O HOH A 222 1555 1555 2.35 LINK CA CA A 102 O HOH A 227 1555 1555 2.37 LINK CA CA A 103 O HOH A 216 1555 1555 2.39 LINK CA CA A 103 O HOH A 216 1555 2455 2.39 SITE 1 AC1 6 HOH A 217 HOH A 218 HOH B 206 HOH B 208 SITE 2 AC1 6 HOH B 219 HOH B 220 SITE 1 AC2 7 U A 4 HOH A 221 HOH A 222 HOH A 227 SITE 2 AC2 7 HOH B 222 HOH B 223 HOH B 229 SITE 1 AC3 7 U A 4 HOH A 221 HOH A 222 HOH A 227 SITE 2 AC3 7 HOH B 222 HOH B 223 HOH B 229 SITE 1 AC4 2 G A 7 HOH A 216 CRYST1 46.810 46.810 53.380 90.00 90.00 120.00 H 3 18 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 0.021363 0.012334 0.000000 0.00000 SCALE2 0.000000 0.024668 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018734 0.00000