HEADER RNA 20-DEC-14 4RZD TITLE CRYSTAL STRUCTURE OF A PREQ1 RIBOSWITCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: PREQ1-III RIBOSWITCH (CLASS 3); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FAECALIBACTERIUM PRAUSNITZII; SOURCE 3 ORGANISM_TAXID: 853 KEYWDS THREE-WAY HELICAL JUNCTION, HL(OUT)-TYPE PSEUDOKNOT, TRANSLATIONAL KEYWDS 2 REGULATION, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.E.WEDEKIND,J.A.LIBERMAN,M.SALIM REVDAT 3 28-FEB-24 4RZD 1 REMARK LINK REVDAT 2 22-JUL-15 4RZD 1 JRNL REVDAT 1 01-JUL-15 4RZD 0 JRNL AUTH J.A.LIBERMAN,K.C.SUDDALA,A.AYTENFISU,D.CHAN,I.A.BELASHOV, JRNL AUTH 2 M.SALIM,D.H.MATHEWS,R.C.SPITALE,N.G.WALTER,J.E.WEDEKIND JRNL TITL STRUCTURAL ANALYSIS OF A CLASS III PREQ1 RIBOSWITCH REVEALS JRNL TITL 2 AN APTAMER DISTANT FROM A RIBOSOME-BINDING SITE REGULATED BY JRNL TITL 3 FAST DYNAMICS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 E3485 2015 JRNL REFN ISSN 0027-8424 JRNL PMID 26106162 JRNL DOI 10.1073/PNAS.1503955112 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 25223 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2526 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 38.2978 - 7.1925 0.89 1263 146 0.1993 0.2153 REMARK 3 2 7.1925 - 5.7150 0.89 1277 142 0.1927 0.1824 REMARK 3 3 5.7150 - 4.9943 0.95 1353 159 0.1704 0.1762 REMARK 3 4 4.9943 - 4.5385 0.86 1238 135 0.1799 0.2510 REMARK 3 5 4.5385 - 4.2136 0.92 1313 149 0.1541 0.1696 REMARK 3 6 4.2136 - 3.9655 0.95 1362 143 0.1675 0.1951 REMARK 3 7 3.9655 - 3.7671 0.96 1374 156 0.1776 0.1946 REMARK 3 8 3.7671 - 3.6032 0.85 1213 139 0.1853 0.2176 REMARK 3 9 3.6032 - 3.4646 0.91 1302 139 0.2193 0.1761 REMARK 3 10 3.4646 - 3.3451 0.94 1351 152 0.2465 0.2624 REMARK 3 11 3.3451 - 3.2406 0.93 1301 147 0.2535 0.3034 REMARK 3 12 3.2406 - 3.1480 0.94 1372 157 0.2695 0.3346 REMARK 3 13 3.1480 - 3.0651 0.93 1367 127 0.3070 0.3137 REMARK 3 14 3.0651 - 2.9904 0.85 1200 140 0.3216 0.3218 REMARK 3 15 2.9904 - 2.9224 0.90 1288 143 0.3613 0.3736 REMARK 3 16 2.9224 - 2.8603 0.85 1223 142 0.4067 0.3585 REMARK 3 17 2.8603 - 2.8031 0.74 1025 109 0.4552 0.5079 REMARK 3 18 2.8031 - 2.7502 0.60 875 101 0.4743 0.5861 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) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 122.0 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 2383 REMARK 3 ANGLE : 0.554 3704 REMARK 3 CHIRALITY : 0.024 494 REMARK 3 PLANARITY : 0.002 100 REMARK 3 DIHEDRAL : 15.736 1186 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 20 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:4) REMARK 3 ORIGIN FOR THE GROUP (A): 37.1079 39.2845 123.2960 REMARK 3 T TENSOR REMARK 3 T11: 1.9962 T22: 1.2440 REMARK 3 T33: 0.4875 T12: 0.2537 REMARK 3 T13: 0.2441 T23: 0.1415 REMARK 3 L TENSOR REMARK 3 L11: 9.8585 L22: 5.1039 REMARK 3 L33: 1.6014 L12: 5.8749 REMARK 3 L13: 3.6358 L23: 1.4699 REMARK 3 S TENSOR REMARK 3 S11: 0.0726 S12: -0.2896 S13: 1.7375 REMARK 3 S21: 0.3699 S22: 0.6023 S23: 1.8278 REMARK 3 S31: -0.3242 S32: -1.7053 S33: -0.6506 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 5:9) REMARK 3 ORIGIN FOR THE GROUP (A): 39.3866 28.9558 107.6021 REMARK 3 T TENSOR REMARK 3 T11: 1.3629 T22: 0.8636 REMARK 3 T33: 0.0639 T12: 0.2264 REMARK 3 T13: -0.0573 T23: 0.0483 REMARK 3 L TENSOR REMARK 3 L11: 5.0869 L22: 4.0699 REMARK 3 L33: 3.2352 L12: -0.7803 REMARK 3 L13: -2.2149 L23: -1.3178 REMARK 3 S TENSOR REMARK 3 S11: -0.0137 S12: -0.7008 S13: -1.4981 REMARK 3 S21: 0.0148 S22: 0.5575 S23: -1.1467 REMARK 3 S31: -0.9794 S32: 0.6054 S33: 0.4974 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 10:14) REMARK 3 ORIGIN FOR THE GROUP (A): 41.5035 36.6475 99.7705 REMARK 3 T TENSOR REMARK 3 T11: 1.3244 T22: 1.0738 REMARK 3 T33: 0.4122 T12: 0.0761 REMARK 3 T13: -0.0834 T23: 0.0721 REMARK 3 L TENSOR REMARK 3 L11: 4.0429 L22: 4.2963 REMARK 3 L33: 5.8469 L12: 0.1615 REMARK 3 L13: -4.7540 L23: -0.0654 REMARK 3 S TENSOR REMARK 3 S11: 1.1965 S12: -0.4682 S13: 0.5163 REMARK 3 S21: 0.1025 S22: -0.2009 S23: 0.1079 REMARK 3 S31: 0.9554 S32: 0.3938 S33: -1.0838 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 15:20) REMARK 3 ORIGIN FOR THE GROUP (A): 33.5230 33.3290 113.7477 REMARK 3 T TENSOR REMARK 3 T11: 0.9908 T22: 0.8835 REMARK 3 T33: 0.3905 T12: 0.1191 REMARK 3 T13: 0.0378 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 1.5848 L22: 9.6044 REMARK 3 L33: 7.8719 L12: -0.0694 REMARK 3 L13: 2.1429 L23: -2.6027 REMARK 3 S TENSOR REMARK 3 S11: -0.1484 S12: -0.2372 S13: -0.0725 REMARK 3 S21: -0.9976 S22: 0.4102 S23: 0.4395 REMARK 3 S31: 0.5882 S32: -0.1180 S33: -0.3667 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 21:24) REMARK 3 ORIGIN FOR THE GROUP (A): 38.6170 31.0438 127.8940 REMARK 3 T TENSOR REMARK 3 T11: 1.2859 T22: 0.9334 REMARK 3 T33: 0.4813 T12: 0.0648 REMARK 3 T13: 0.1518 T23: -0.1430 REMARK 3 L TENSOR REMARK 3 L11: 7.2643 L22: 5.1327 REMARK 3 L33: 4.4109 L12: -5.2236 REMARK 3 L13: -4.5057 L23: 4.6968 REMARK 3 S TENSOR REMARK 3 S11: 0.8581 S12: 0.2204 S13: 0.9062 REMARK 3 S21: -0.4780 S22: 0.0401 S23: -0.5287 REMARK 3 S31: -0.7227 S32: -0.7228 S33: -0.8498 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 25:28) REMARK 3 ORIGIN FOR THE GROUP (A): 27.0777 37.0813 138.2514 REMARK 3 T TENSOR REMARK 3 T11: 1.6741 T22: 1.6510 REMARK 3 T33: 0.7768 T12: 0.1749 REMARK 3 T13: 0.2523 T23: -0.0452 REMARK 3 L TENSOR REMARK 3 L11: 2.1182 L22: 6.3450 REMARK 3 L33: 2.9436 L12: -3.5345 REMARK 3 L13: 1.7214 L23: -3.7675 REMARK 3 S TENSOR REMARK 3 S11: -0.4864 S12: -2.7558 S13: 0.1866 REMARK 3 S21: 0.2431 S22: 2.2510 S23: 0.2475 REMARK 3 S31: 0.5130 S32: 0.0335 S33: -1.8183 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 29:32) REMARK 3 ORIGIN FOR THE GROUP (A): 27.8178 25.0148 148.1332 REMARK 3 T TENSOR REMARK 3 T11: 1.8711 T22: 2.9373 REMARK 3 T33: 1.2040 T12: 0.0528 REMARK 3 T13: -0.0679 T23: 0.5015 REMARK 3 L TENSOR REMARK 3 L11: 9.1976 L22: 2.0018 REMARK 3 L33: 9.2889 L12: -7.1088 REMARK 3 L13: 9.1756 L23: -6.2372 REMARK 3 S TENSOR REMARK 3 S11: 2.4933 S12: -0.1372 S13: -0.9713 REMARK 3 S21: 0.3683 S22: 1.6748 S23: 2.3521 REMARK 3 S31: 1.0587 S32: 0.7088 S33: -3.3768 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 33:41) REMARK 3 ORIGIN FOR THE GROUP (A): 29.5826 30.8837 155.9265 REMARK 3 T TENSOR REMARK 3 T11: 2.8272 T22: 2.1839 REMARK 3 T33: 1.6393 T12: 0.2254 REMARK 3 T13: 0.3860 T23: -0.0690 REMARK 3 L TENSOR REMARK 3 L11: 2.2044 L22: 3.6950 REMARK 3 L33: 2.5652 L12: 2.6377 REMARK 3 L13: -1.6162 L23: -2.7496 REMARK 3 S TENSOR REMARK 3 S11: 2.2184 S12: 1.2947 S13: 0.2225 REMARK 3 S21: 0.8013 S22: -1.2439 S23: 2.5724 REMARK 3 S31: -1.6212 S32: -0.3939 S33: -0.7622 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 42:45) REMARK 3 ORIGIN FOR THE GROUP (A): 33.9241 26.5048 142.0879 REMARK 3 T TENSOR REMARK 3 T11: 1.6108 T22: 2.0861 REMARK 3 T33: 0.7456 T12: 0.2018 REMARK 3 T13: 0.0482 T23: -0.1370 REMARK 3 L TENSOR REMARK 3 L11: 1.9814 L22: 4.9546 REMARK 3 L33: 5.4303 L12: 4.7290 REMARK 3 L13: 6.2753 L23: 4.7864 REMARK 3 S TENSOR REMARK 3 S11: -1.7542 S12: -1.1255 S13: -0.4880 REMARK 3 S21: -2.1836 S22: -0.4763 S23: 1.0371 REMARK 3 S31: -0.6017 S32: -2.7687 S33: 2.3623 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 46:49) REMARK 3 ORIGIN FOR THE GROUP (A): 24.3302 32.7553 131.2186 REMARK 3 T TENSOR REMARK 3 T11: 1.5370 T22: 1.4963 REMARK 3 T33: 0.7123 T12: 0.0489 REMARK 3 T13: 0.0675 T23: 0.2270 REMARK 3 L TENSOR REMARK 3 L11: 6.2434 L22: 6.0806 REMARK 3 L33: 5.2782 L12: -5.5453 REMARK 3 L13: 0.9434 L23: 0.0150 REMARK 3 S TENSOR REMARK 3 S11: 0.5131 S12: 1.3123 S13: -0.6868 REMARK 3 S21: -0.2367 S22: 0.9430 S23: 1.0839 REMARK 3 S31: -0.6461 S32: 1.6580 S33: -1.4248 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 50:54) REMARK 3 ORIGIN FOR THE GROUP (A): 24.3276 38.9796 112.2155 REMARK 3 T TENSOR REMARK 3 T11: 1.2381 T22: 1.3541 REMARK 3 T33: 0.8944 T12: 0.4415 REMARK 3 T13: 0.2089 T23: 0.3620 REMARK 3 L TENSOR REMARK 3 L11: 0.9973 L22: 4.3662 REMARK 3 L33: 6.1497 L12: 2.0279 REMARK 3 L13: -2.0995 L23: -5.0353 REMARK 3 S TENSOR REMARK 3 S11: -0.1470 S12: -1.6646 S13: -1.0778 REMARK 3 S21: 1.3443 S22: -0.6108 S23: 1.3185 REMARK 3 S31: -1.1279 S32: 0.2939 S33: 0.6257 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 55:62) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1253 48.2741 107.4996 REMARK 3 T TENSOR REMARK 3 T11: 0.9472 T22: 0.8347 REMARK 3 T33: 0.5484 T12: 0.1904 REMARK 3 T13: -0.1596 T23: -0.0736 REMARK 3 L TENSOR REMARK 3 L11: 1.2654 L22: 8.8151 REMARK 3 L33: 3.7343 L12: 1.2285 REMARK 3 L13: -2.1713 L23: 0.1457 REMARK 3 S TENSOR REMARK 3 S11: 0.1623 S12: 0.4149 S13: -0.1375 REMARK 3 S21: 1.1034 S22: -0.3908 S23: 0.6887 REMARK 3 S31: -0.3276 S32: 0.1248 S33: 0.2017 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 63:68) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4455 64.5836 102.4823 REMARK 3 T TENSOR REMARK 3 T11: 1.2849 T22: 1.1061 REMARK 3 T33: 0.6832 T12: 0.3358 REMARK 3 T13: -0.0765 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 6.0228 L22: 1.3749 REMARK 3 L33: 1.5980 L12: 2.5864 REMARK 3 L13: -1.4929 L23: -0.4154 REMARK 3 S TENSOR REMARK 3 S11: -1.1104 S12: -1.1235 S13: 1.0721 REMARK 3 S21: -0.7115 S22: 0.5309 S23: 0.6391 REMARK 3 S31: -0.2148 S32: -0.1016 S33: 0.5561 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 69:75) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0433 53.7053 100.1202 REMARK 3 T TENSOR REMARK 3 T11: 1.0105 T22: 0.9692 REMARK 3 T33: 0.5149 T12: 0.1139 REMARK 3 T13: -0.0469 T23: 0.0937 REMARK 3 L TENSOR REMARK 3 L11: 8.6938 L22: 4.6067 REMARK 3 L33: 3.0197 L12: 0.5115 REMARK 3 L13: 5.1294 L23: 0.1272 REMARK 3 S TENSOR REMARK 3 S11: 0.0757 S12: 0.8823 S13: -0.2570 REMARK 3 S21: 0.1171 S22: 0.2389 S23: 0.4888 REMARK 3 S31: 0.3098 S32: 0.8155 S33: -0.1678 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 76:79) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3729 44.4360 115.4991 REMARK 3 T TENSOR REMARK 3 T11: 1.1648 T22: 0.8663 REMARK 3 T33: 0.5527 T12: 0.1982 REMARK 3 T13: 0.0718 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 3.1535 L22: 5.9172 REMARK 3 L33: 5.0126 L12: -1.0258 REMARK 3 L13: 3.5285 L23: 0.9861 REMARK 3 S TENSOR REMARK 3 S11: 0.3170 S12: -0.2410 S13: -1.0694 REMARK 3 S21: 0.2542 S22: 0.7241 S23: 0.6812 REMARK 3 S31: 0.5599 S32: -0.2306 S33: -0.7039 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: (CHAIN A AND RESID 80:83) REMARK 3 ORIGIN FOR THE GROUP (A): 13.1960 33.3122 109.1728 REMARK 3 T TENSOR REMARK 3 T11: 1.1007 T22: 0.8014 REMARK 3 T33: 1.0174 T12: 0.0804 REMARK 3 T13: 0.0747 T23: 0.0513 REMARK 3 L TENSOR REMARK 3 L11: 8.1293 L22: 6.3005 REMARK 3 L33: 1.8113 L12: -2.0352 REMARK 3 L13: -1.1577 L23: -1.2392 REMARK 3 S TENSOR REMARK 3 S11: 0.4515 S12: -0.4918 S13: -0.8839 REMARK 3 S21: 1.0835 S22: -0.8422 S23: -0.9557 REMARK 3 S31: -0.5131 S32: 0.0596 S33: 0.5391 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: (CHAIN A AND RESID 84:88) REMARK 3 ORIGIN FOR THE GROUP (A): 30.0723 36.8036 103.6932 REMARK 3 T TENSOR REMARK 3 T11: 0.9855 T22: 0.8407 REMARK 3 T33: 0.5048 T12: 0.2566 REMARK 3 T13: -0.0428 T23: 0.1105 REMARK 3 L TENSOR REMARK 3 L11: 8.6653 L22: 8.1155 REMARK 3 L33: 8.4181 L12: 5.5562 REMARK 3 L13: -4.7607 L23: -0.7227 REMARK 3 S TENSOR REMARK 3 S11: 1.0173 S12: -0.4894 S13: -0.2187 REMARK 3 S21: 0.6811 S22: -0.6714 S23: 0.2832 REMARK 3 S31: -0.0988 S32: 0.7573 S33: -0.3914 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: (CHAIN A AND RESID 89:92) REMARK 3 ORIGIN FOR THE GROUP (A): 43.6209 43.2932 93.3331 REMARK 3 T TENSOR REMARK 3 T11: 1.3702 T22: 1.0277 REMARK 3 T33: 0.5111 T12: 0.0294 REMARK 3 T13: -0.0343 T23: 0.0395 REMARK 3 L TENSOR REMARK 3 L11: 3.1478 L22: 4.3597 REMARK 3 L33: 6.6517 L12: 3.5928 REMARK 3 L13: -0.1060 L23: 1.0474 REMARK 3 S TENSOR REMARK 3 S11: 0.5326 S12: 0.1170 S13: 0.3397 REMARK 3 S21: 0.6029 S22: 0.4876 S23: -0.2337 REMARK 3 S31: -0.2880 S32: -0.7042 S33: -1.0625 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: (CHAIN A AND RESID 93:96) REMARK 3 ORIGIN FOR THE GROUP (A): 53.3199 28.4798 93.3761 REMARK 3 T TENSOR REMARK 3 T11: 1.2800 T22: 1.5350 REMARK 3 T33: 0.8069 T12: 0.1198 REMARK 3 T13: -0.1598 T23: 0.3006 REMARK 3 L TENSOR REMARK 3 L11: 3.6295 L22: 0.2939 REMARK 3 L33: 3.3883 L12: -0.7236 REMARK 3 L13: -3.5117 L23: 0.5054 REMARK 3 S TENSOR REMARK 3 S11: -1.3769 S12: -1.3598 S13: -1.0728 REMARK 3 S21: 0.8467 S22: 1.1784 S23: -0.4169 REMARK 3 S31: -0.5665 S32: 1.6525 S33: 0.3677 REMARK 3 TLS GROUP : 20 REMARK 3 SELECTION: (CHAIN A AND RESID 97:101) REMARK 3 ORIGIN FOR THE GROUP (A): 69.0956 26.4555 91.0341 REMARK 3 T TENSOR REMARK 3 T11: 1.4695 T22: 1.8484 REMARK 3 T33: 1.8102 T12: -0.0268 REMARK 3 T13: -0.2148 T23: 0.3387 REMARK 3 L TENSOR REMARK 3 L11: 3.1415 L22: 4.1572 REMARK 3 L33: 3.3450 L12: -3.0503 REMARK 3 L13: 2.8130 L23: -1.8470 REMARK 3 S TENSOR REMARK 3 S11: -1.0576 S12: -0.5783 S13: -0.4294 REMARK 3 S21: 0.4516 S22: 0.1675 S23: -0.8167 REMARK 3 S31: -1.2660 S32: 1.4929 S33: 1.2363 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 4RZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000087984. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-10 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 : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1696 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : RH COATED FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25223 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 46.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85% TACSIMATE PH 7.0, 0.010 M REMARK 280 MG(C2H3O2)2, 0.006 M CO(NH3)6CL3, AND 0.001 M SPERMINE HCL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 185.57667 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 92.78833 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 139.18250 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 46.39417 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 231.97083 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 185.57667 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 92.78833 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 46.39417 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 139.18250 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 231.97083 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 C A 34 REMARK 465 U A 35 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 C A 36 P OP1 OP2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HO2' A A 38 O4' A A 39 1.51 REMARK 500 REMARK 500 REMARK: NULL 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 GTP A 1 C3' - O3' - P ANGL. DEV. = -11.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PRF A 201 DBREF 4RZD A 1 101 PDB 4RZD 4RZD 1 101 SEQRES 1 A 101 GTP A G C A A C U U A G G A SEQRES 2 A 101 U U U U A G G C U C C C C SEQRES 3 A 101 G G C G U G U C U C G A A SEQRES 4 A 101 C C A U G C C G G G C C A SEQRES 5 A 101 A A C C C A U A G G G C U SEQRES 6 A 101 G G C G G U C C C U G U G SEQRES 7 A 101 C G G U C A A A A U U C A SEQRES 8 A 101 U C C G C C G G A G MODRES 4RZD GTP A 1 G GUANOSINE-5'-TRIPHOSPHATE HET GTP A 1 41 HET PRF A 201 22 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM PRF 7-DEAZA-7-AMINOMETHYL-GUANINE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 PRF C7 H9 N5 O FORMUL 3 HOH *4(H2 O) LINK O3' GTP A 1 P A A 2 1555 1555 1.61 SITE 1 AC1 7 C A 7 U A 8 U A 17 A A 18 SITE 2 AC1 7 A A 84 A A 85 HOH A 304 CRYST1 84.083 84.083 278.365 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 0.011893 0.006866 0.000000 0.00000 SCALE2 0.000000 0.013733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003592 0.00000 HETATM 1 PG GTP A 1 29.273 45.854 128.374 1.00241.65 P ANISOU 1 PG GTP A 1 32547 30445 28824 5386 5931 -1269 P HETATM 2 O1G GTP A 1 30.661 45.258 128.350 1.00205.52 O ANISOU 2 O1G GTP A 1 29028 25916 23144 5066 5728 -1084 O HETATM 3 O2G GTP A 1 28.882 46.172 129.798 1.00229.37 O ANISOU 3 O2G GTP A 1 30568 29277 27304 5430 6799 -2303 O HETATM 4 O3G GTP A 1 28.292 44.871 127.782 1.00237.65 O ANISOU 4 O3G GTP A 1 31776 30362 28158 5094 5667 -616 O HETATM 5 O3B GTP A 1 29.278 47.208 127.501 1.00270.10 O ANISOU 5 O3B GTP A 1 35725 33125 33775 5935 5457 -1066 O HETATM 6 PB GTP A 1 29.601 47.169 125.923 1.00206.38 P ANISOU 6 PB GTP A 1 27950 24624 25841 5858 4516 11 P HETATM 7 O1B GTP A 1 29.550 48.573 125.368 1.00201.64 O ANISOU 7 O1B GTP A 1 26861 23167 26587 6329 4120 110 O HETATM 8 O2B GTP A 1 30.949 46.540 125.665 1.00176.35 O ANISOU 8 O2B GTP A 1 25189 20932 20884 5506 4293 261 O HETATM 9 O3A GTP A 1 28.413 46.282 125.287 1.00225.18 O ANISOU 9 O3A GTP A 1 29918 27419 28220 5598 4255 655 O HETATM 10 PA GTP A 1 28.767 45.188 124.161 1.00194.43 P ANISOU 10 PA GTP A 1 26650 23785 23439 5097 3623 1574 P HETATM 11 O1A GTP A 1 27.509 44.516 123.666 1.00202.11 O ANISOU 11 O1A GTP A 1 27095 25098 24599 4920 3424 2088 O HETATM 12 O2A GTP A 1 29.561 45.794 123.028 1.00170.52 O ANISOU 12 O2A GTP A 1 23957 20210 20624 5105 2940 2139 O HETATM 13 O5' GTP A 1 29.661 44.157 125.010 1.00169.64 O ANISOU 13 O5' GTP A 1 24319 21185 18953 4727 4027 1180 O HETATM 14 C5' GTP A 1 30.374 43.092 124.429 1.00143.26 C ANISOU 14 C5' GTP A 1 21695 18095 14643 4272 3655 1627 C HETATM 15 C4' GTP A 1 31.514 42.810 125.400 1.00129.94 C ANISOU 15 C4' GTP A 1 20696 16529 12148 4144 4023 1054 C HETATM 16 O4' GTP A 1 31.193 41.768 126.299 1.00135.26 O ANISOU 16 O4' GTP A 1 21450 17815 12127 3802 4381 836 O HETATM 17 C3' GTP A 1 32.800 42.364 124.729 1.00122.41 C ANISOU 17 C3' GTP A 1 20534 15438 10539 3879 3589 1312 C HETATM 18 O3' GTP A 1 33.531 43.444 124.197 1.00126.04 O ANISOU 18 O3' GTP A 1 21122 15327 11440 4146 3361 1337 O HETATM 19 C2' GTP A 1 33.519 41.675 125.869 1.00127.25 C ANISOU 19 C2' GTP A 1 21677 16339 10331 3640 3958 811 C HETATM 20 O2' GTP A 1 34.354 42.585 126.550 1.00119.08 O ANISOU 20 O2' GTP A 1 20878 14962 9405 3910 4258 258 O HETATM 21 C1' GTP A 1 32.389 41.167 126.759 1.00127.31 C ANISOU 21 C1' GTP A 1 21226 16888 10257 3512 4388 636 C HETATM 22 N9 GTP A 1 32.293 39.704 126.637 1.00120.25 N ANISOU 22 N9 GTP A 1 20603 16448 8639 2997 4137 998 N HETATM 23 C8 GTP A 1 31.197 38.982 126.244 1.00122.31 C ANISOU 23 C8 GTP A 1 20452 17074 8945 2802 3986 1433 C HETATM 24 N7 GTP A 1 31.518 37.667 126.272 1.00118.21 N ANISOU 24 N7 GTP A 1 20357 16855 7702 2317 3725 1648 N HETATM 25 C5 GTP A 1 32.798 37.542 126.687 1.00113.79 C ANISOU 25 C5 GTP A 1 20449 16108 6679 2203 3696 1352 C HETATM 26 C6 GTP A 1 33.618 36.442 126.896 1.00111.79 C ANISOU 26 C6 GTP A 1 20219 15874 6383 1591 3146 1279 C HETATM 27 O6 GTP A 1 33.190 35.307 126.691 1.00108.63 O ANISOU 27 O6 GTP A 1 19629 15771 5877 1186 2809 1578 O HETATM 28 N1 GTP A 1 34.913 36.636 127.335 1.00105.74 N ANISOU 28 N1 GTP A 1 19582 14784 5812 1487 2974 887 N HETATM 29 C2 GTP A 1 35.386 37.912 127.563 1.00106.55 C ANISOU 29 C2 GTP A 1 19879 14539 6065 1921 3318 558 C HETATM 30 N2 GTP A 1 36.633 38.100 127.984 1.00103.23 N ANISOU 30 N2 GTP A 1 19553 13810 5862 1808 3129 240 N HETATM 31 N3 GTP A 1 34.565 38.997 127.352 1.00111.16 N ANISOU 31 N3 GTP A 1 20522 15089 6626 2534 3885 578 N HETATM 32 C4 GTP A 1 33.294 38.814 126.925 1.00114.86 C ANISOU 32 C4 GTP A 1 20599 15850 7192 2623 3974 947 C HETATM 33 H4' GTP A 1 31.719 43.722 125.960 1.00155.93 H HETATM 34 H3' GTP A 1 32.570 41.634 123.953 1.00146.90 H HETATM 35 H2' GTP A 1 34.092 40.832 125.485 1.00152.70 H HETATM 36 HO2' GTP A 1 34.029 42.703 127.468 1.00142.89 H HETATM 37 H1' GTP A 1 32.587 41.452 127.792 1.00152.77 H HETATM 38 H8 GTP A 1 30.230 39.397 125.957 1.00146.77 H HETATM 39 HN1 GTP A 1 35.534 35.817 127.494 1.00126.89 H HETATM 40 HN21 GTP A 1 36.976 39.041 128.149 1.00123.88 H HETATM 41 HN22 GTP A 1 37.242 37.304 128.139 1.00123.88 H