HEADER RNA 21-JAN-14 4OJI TITLE CRYSTAL STRUCTURE OF TWISTER RIBOZYME CAVEAT 4OJI THE CALCULATED R_FREE(0.1680) IS SMALLER THAN R_WORK(0.1753) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (52-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC RNA SAMPLE ACCORDING TO O.SATIVA SEQUENCE. KEYWDS PSEUDOKNOT, SELF-CLEAVAGE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,T.J.WILSON,S.A.MCPHEE,D.M.J.LILLEY REVDAT 3 03-SEP-14 4OJI 1 JRNL REVDAT 2 27-AUG-14 4OJI 1 JRNL REVDAT 1 23-JUL-14 4OJI 0 JRNL AUTH Y.LIU,T.J.WILSON,S.A.MCPHEE,D.M.LILLEY JRNL TITL CRYSTAL STRUCTURE AND MECHANISTIC INVESTIGATION OF THE JRNL TITL 2 TWISTER RIBOZYME. JRNL REF NAT.CHEM.BIOL. V. 10 739 2014 JRNL REFN ISSN 1552-4450 JRNL PMID 25038788 JRNL DOI 10.1038/NCHEMBIO.1587 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 7646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.620 REMARK 3 FREE R VALUE TEST SET COUNT : 353 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 47.9708 - 3.3173 0.98 2562 116 0.1506 0.1603 REMARK 3 2 3.3173 - 2.6331 0.99 2381 121 0.2059 0.2306 REMARK 3 3 2.6331 - 2.3003 1.00 2350 116 0.2653 0.3570 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.89 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 : 0.003 1291 REMARK 3 ANGLE : 0.633 2013 REMARK 3 CHIRALITY : 0.030 266 REMARK 3 PLANARITY : 0.003 54 REMARK 3 DIHEDRAL : 14.234 643 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 4OJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB084571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : PH8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 47.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, AMMONIUM ACETATE, MAGNESIUM REMARK 280 CHLORIDE, , PH PH8, EVAPORATION, TEMPERATURE 280K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 116.98067 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 58.49033 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 87.73550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.24517 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 146.22583 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 116.98067 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 58.49033 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 29.24517 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 87.73550 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 146.22583 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 A A 17 REMARK 465 U A 18 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 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 245 O REMARK 620 2 HOH A 246 O 177.1 REMARK 620 3 HOH A 249 O 92.0 89.8 REMARK 620 4 HOH A 248 O 92.2 89.9 96.6 REMARK 620 5 HOH A 250 O 89.9 87.9 86.4 176.3 REMARK 620 6 HOH A 247 O 85.9 92.1 175.3 87.6 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 209 O REMARK 620 2 HOH A 212 O 85.7 REMARK 620 3 HOH A 213 O 90.4 89.7 REMARK 620 4 HOH A 210 O 97.4 171.9 82.8 REMARK 620 5 DU A 6 OP1 90.2 90.6 179.3 96.9 REMARK 620 6 HOH A 211 O 176.1 91.0 91.5 86.1 87.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 207 O REMARK 620 2 HOH A 208 O 98.8 REMARK 620 3 C A 26 OP1 100.0 96.2 REMARK 620 4 U A 24 OP2 82.7 159.4 103.8 REMARK 620 5 HOH A 205 O 167.7 83.7 91.6 90.7 REMARK 620 6 HOH A 206 O 81.8 84.4 178.0 75.4 86.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 225 O REMARK 620 2 HOH A 228 O 105.4 REMARK 620 3 HOH A 223 O 93.2 76.8 REMARK 620 4 HOH A 226 O 111.9 139.2 85.2 REMARK 620 5 HOH A 224 O 175.4 70.0 85.1 72.3 REMARK 620 6 HOH A 227 O 107.3 93.9 159.2 90.2 74.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 230 O REMARK 620 2 HOH A 229 O 130.3 REMARK 620 3 HOH A 244 O 63.9 67.5 REMARK 620 4 HOH A 222 O 73.2 74.1 59.5 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 MG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 105 DBREF 4OJI A 1 54 PDB 4OJI 4OJI 1 54 SEQRES 1 A 54 C C G C C DU A A C A C U G SEQRES 2 A 54 C C A A U G C C G G U C C SEQRES 3 A 54 C A A G C C C G G A U A A SEQRES 4 A 54 A A G U G G A G G G G G C SEQRES 5 A 54 G G HET MG A 101 1 HET MG A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 5(MG 2+) FORMUL 7 HOH *50(H2 O) LINK MG MG A 101 O HOH A 245 1555 1555 1.94 LINK MG MG A 105 O HOH A 209 1555 1555 1.96 LINK MG MG A 104 O HOH A 207 1555 1555 1.97 LINK MG MG A 101 O HOH A 246 1555 1555 1.97 LINK MG MG A 105 O HOH A 212 1555 1555 1.98 LINK MG MG A 102 O HOH A 225 1555 1555 1.98 LINK MG MG A 104 O HOH A 208 1555 1555 2.00 LINK MG MG A 101 O HOH A 249 1555 1555 2.01 LINK OP1 C A 26 MG MG A 104 1555 1555 2.04 LINK MG MG A 105 O HOH A 213 1555 1555 2.04 LINK MG MG A 105 O HOH A 210 1555 1555 2.04 LINK MG MG A 101 O HOH A 248 1555 1555 2.05 LINK OP1 DU A 6 MG MG A 105 1555 1555 2.06 LINK MG MG A 102 O HOH A 228 1555 1555 2.11 LINK OP2 U A 24 MG MG A 104 1555 1555 2.13 LINK MG MG A 101 O HOH A 250 1555 1555 2.16 LINK MG MG A 104 O HOH A 205 1555 1555 2.17 LINK MG MG A 102 O HOH A 223 1555 1555 2.19 LINK MG MG A 101 O HOH A 247 1555 1555 2.19 LINK MG MG A 105 O HOH A 211 1555 1555 2.20 LINK MG MG A 103 O HOH A 230 1555 1555 2.24 LINK MG MG A 102 O HOH A 226 1555 1555 2.28 LINK MG MG A 104 O HOH A 206 1555 1555 2.31 LINK MG MG A 103 O HOH A 229 1555 1555 2.32 LINK MG MG A 102 O HOH A 224 1555 1555 2.39 LINK MG MG A 102 O HOH A 227 1555 1555 2.47 LINK MG MG A 103 O HOH A 244 1555 1555 2.65 LINK MG MG A 103 O HOH A 222 1555 1555 2.84 SITE 1 AC1 6 HOH A 245 HOH A 246 HOH A 247 HOH A 248 SITE 2 AC1 6 HOH A 249 HOH A 250 SITE 1 AC2 6 HOH A 223 HOH A 224 HOH A 225 HOH A 226 SITE 2 AC2 6 HOH A 227 HOH A 228 SITE 1 AC3 4 HOH A 222 HOH A 229 HOH A 230 HOH A 244 SITE 1 AC4 7 U A 24 C A 25 C A 26 HOH A 205 SITE 2 AC4 7 HOH A 206 HOH A 207 HOH A 208 SITE 1 AC5 6 DU A 6 HOH A 209 HOH A 210 HOH A 211 SITE 2 AC5 6 HOH A 212 HOH A 213 CRYST1 55.380 55.380 175.471 90.00 90.00 120.00 P 65 2 2 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 0.018057 0.010425 0.000000 0.00000 SCALE2 0.000000 0.020850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005699 0.00000 MASTER 310 0 5 0 0 0 9 6 0 0 0 5 END