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 4 28-FEB-24 4OJI 1 REMARK LINK 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 1.8.4_1496 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) : 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 DEPOSITION ID IS D_1000084571. 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 0.2.8 REMARK 200 DATA SCALING SOFTWARE : SCALA 0.2.8 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 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DU A 6 OP1 REMARK 620 2 HOH A 209 O 90.2 REMARK 620 3 HOH A 210 O 96.9 97.4 REMARK 620 4 HOH A 211 O 87.8 176.1 86.1 REMARK 620 5 HOH A 212 O 90.6 85.7 171.9 91.0 REMARK 620 6 HOH A 213 O 179.3 90.4 82.8 91.5 89.7 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 U A 24 OP2 REMARK 620 2 C A 26 OP1 103.8 REMARK 620 3 HOH A 205 O 90.7 91.6 REMARK 620 4 HOH A 206 O 75.4 178.0 86.5 REMARK 620 5 HOH A 207 O 82.7 100.0 167.7 81.8 REMARK 620 6 HOH A 208 O 159.4 96.2 83.7 84.4 98.8 REMARK 620 N 1 2 3 4 5 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 247 O 85.9 92.1 REMARK 620 4 HOH A 248 O 92.2 89.9 87.6 REMARK 620 5 HOH A 249 O 92.0 89.8 175.3 96.6 REMARK 620 6 HOH A 250 O 89.9 87.9 89.4 176.3 86.4 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 223 O REMARK 620 2 HOH A 224 O 85.1 REMARK 620 3 HOH A 225 O 93.2 175.4 REMARK 620 4 HOH A 226 O 85.2 72.3 111.9 REMARK 620 5 HOH A 227 O 159.2 74.2 107.3 90.2 REMARK 620 6 HOH A 228 O 76.8 70.0 105.4 139.2 93.9 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 222 O REMARK 620 2 HOH A 229 O 74.1 REMARK 620 3 HOH A 230 O 73.2 130.3 REMARK 620 4 HOH A 244 O 59.5 67.5 63.9 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 OP1 DU A 6 MG MG A 105 1555 1555 2.06 LINK OP2 U A 24 MG MG A 104 1555 1555 2.13 LINK OP1 C A 26 MG MG A 104 1555 1555 2.04 LINK MG MG A 101 O HOH A 245 1555 1555 1.94 LINK MG MG A 101 O HOH A 246 1555 1555 1.97 LINK MG MG A 101 O HOH A 247 1555 1555 2.19 LINK MG MG A 101 O HOH A 248 1555 1555 2.05 LINK MG MG A 101 O HOH A 249 1555 1555 2.01 LINK MG MG A 101 O HOH A 250 1555 1555 2.16 LINK MG MG A 102 O HOH A 223 1555 1555 2.19 LINK MG MG A 102 O HOH A 224 1555 1555 2.39 LINK MG MG A 102 O HOH A 225 1555 1555 1.98 LINK MG MG A 102 O HOH A 226 1555 1555 2.28 LINK MG MG A 102 O HOH A 227 1555 1555 2.47 LINK MG MG A 102 O HOH A 228 1555 1555 2.11 LINK MG MG A 103 O HOH A 222 1555 1555 2.84 LINK MG MG A 103 O HOH A 229 1555 1555 2.32 LINK MG MG A 103 O HOH A 230 1555 1555 2.24 LINK MG MG A 103 O HOH A 244 1555 1555 2.65 LINK MG MG A 104 O HOH A 205 1555 1555 2.17 LINK MG MG A 104 O HOH A 206 1555 1555 2.31 LINK MG MG A 104 O HOH A 207 1555 1555 1.97 LINK MG MG A 104 O HOH A 208 1555 1555 2.00 LINK MG MG A 105 O HOH A 209 1555 1555 1.96 LINK MG MG A 105 O HOH A 210 1555 1555 2.04 LINK MG MG A 105 O HOH A 211 1555 1555 2.20 LINK MG MG A 105 O HOH A 212 1555 1555 1.98 LINK MG MG A 105 O HOH A 213 1555 1555 2.04 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