HEADER RNA 05-JUN-22 8D5L TITLE CRYSTAL STRUCTURE OF THEOPHYLLINE APTAMER IN COMPLEX WITH TAL1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (33-MER); 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, APTAMER, THEOPHYLLINE EXPDTA X-RAY DIFFRACTION AUTHOR E.MENICHELLI,G.SPRAGGON REVDAT 2 25-OCT-23 8D5L 1 REMARK REVDAT 1 30-NOV-22 8D5L 0 JRNL AUTH E.MENICHELLI,B.J.LAM,Y.WANG,V.S.WANG,J.SHAFFER,K.F.TJHUNG, JRNL AUTH 2 B.BURSULAYA,T.N.NGUYEN,T.VO,P.B.ALPER,C.S.MCALLISTER, JRNL AUTH 3 D.H.JONES,G.SPRAGGON,P.Y.MICHELLYS,J.JOSLIN,G.F.JOYCE, JRNL AUTH 4 J.ROGERS JRNL TITL DISCOVERY OF SMALL MOLECULES THAT TARGET A JRNL TITL 2 TERTIARY-STRUCTURED RNA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 17119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 36413497 JRNL DOI 10.1073/PNAS.2213117119 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 46389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 2165 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 41.0600 - 4.0500 0.99 3002 187 0.1618 0.1681 REMARK 3 2 4.0500 - 3.2200 0.97 2987 135 0.1526 0.1635 REMARK 3 3 3.2200 - 2.8100 0.98 3049 93 0.1757 0.1878 REMARK 3 4 2.8100 - 2.5500 0.98 2993 144 0.2080 0.2714 REMARK 3 5 2.5500 - 2.3700 0.97 3029 132 0.2190 0.3075 REMARK 3 6 2.3700 - 2.2300 0.97 2977 167 0.2134 0.2566 REMARK 3 7 2.2300 - 2.1200 0.96 2863 175 0.2022 0.2556 REMARK 3 8 2.1200 - 2.0300 0.95 2915 193 0.2069 0.2360 REMARK 3 9 2.0300 - 1.9500 0.95 2887 135 0.2188 0.2425 REMARK 3 10 1.9500 - 1.8800 0.95 2941 126 0.2193 0.2741 REMARK 3 11 1.8800 - 1.8200 0.95 2946 129 0.2303 0.2445 REMARK 3 12 1.8200 - 1.7700 0.94 2934 138 0.2328 0.2756 REMARK 3 13 1.7700 - 1.7200 0.94 2876 144 0.2431 0.3117 REMARK 3 14 1.7200 - 1.6800 0.94 2908 137 0.2480 0.2711 REMARK 3 15 1.6800 - 1.6400 0.94 2917 130 0.2807 0.3281 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.87 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4445 13.7863 32.8705 REMARK 3 T TENSOR REMARK 3 T11: 0.1752 T22: 0.1413 REMARK 3 T33: 0.1825 T12: 0.0057 REMARK 3 T13: -0.0176 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 0.0283 L22: 0.0286 REMARK 3 L33: 0.0407 L12: 0.0130 REMARK 3 L13: -0.0299 L23: 0.0123 REMARK 3 S TENSOR REMARK 3 S11: 0.0753 S12: 0.0072 S13: -0.0045 REMARK 3 S21: 0.0123 S22: -0.1726 S23: 0.0514 REMARK 3 S31: -0.0029 S32: 0.0895 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.6689 28.0133 17.4810 REMARK 3 T TENSOR REMARK 3 T11: 0.8154 T22: 0.2628 REMARK 3 T33: 0.2196 T12: -0.0345 REMARK 3 T13: -0.0697 T23: 0.2779 REMARK 3 L TENSOR REMARK 3 L11: 0.0327 L22: 0.0260 REMARK 3 L33: 0.0570 L12: 0.0261 REMARK 3 L13: 0.0100 L23: 0.0276 REMARK 3 S TENSOR REMARK 3 S11: 0.1369 S12: 0.0572 S13: 0.0370 REMARK 3 S21: -0.1873 S22: 0.1043 S23: 0.0984 REMARK 3 S31: -0.0432 S32: -0.0132 S33: 0.1575 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 21 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4290 14.5590 37.0314 REMARK 3 T TENSOR REMARK 3 T11: 0.1376 T22: 0.0933 REMARK 3 T33: 0.1959 T12: 0.0089 REMARK 3 T13: -0.0110 T23: -0.0211 REMARK 3 L TENSOR REMARK 3 L11: 0.0783 L22: 0.0569 REMARK 3 L33: 0.0011 L12: -0.0220 REMARK 3 L13: -0.0087 L23: 0.0235 REMARK 3 S TENSOR REMARK 3 S11: 0.0308 S12: -0.0552 S13: -0.0676 REMARK 3 S21: -0.0321 S22: -0.0179 S23: 0.0740 REMARK 3 S31: 0.0362 S32: 0.0278 S33: -0.0009 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6545 4.3942 14.4866 REMARK 3 T TENSOR REMARK 3 T11: 0.1611 T22: 0.2578 REMARK 3 T33: 0.1440 T12: -0.0227 REMARK 3 T13: 0.0145 T23: 0.0268 REMARK 3 L TENSOR REMARK 3 L11: 0.0701 L22: 0.0491 REMARK 3 L33: 0.0408 L12: -0.0069 REMARK 3 L13: -0.0251 L23: 0.0627 REMARK 3 S TENSOR REMARK 3 S11: -0.0456 S12: 0.1076 S13: 0.0432 REMARK 3 S21: -0.0095 S22: 0.0895 S23: -0.0395 REMARK 3 S31: -0.1306 S32: -0.0753 S33: 0.0004 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6766 0.7596 16.3329 REMARK 3 T TENSOR REMARK 3 T11: 0.1455 T22: 0.2533 REMARK 3 T33: 0.1717 T12: -0.0234 REMARK 3 T13: 0.0153 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.0788 L22: 0.1226 REMARK 3 L33: 0.0865 L12: -0.0591 REMARK 3 L13: -0.0162 L23: 0.1235 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: 0.1674 S13: -0.0229 REMARK 3 S21: -0.0512 S22: -0.0340 S23: -0.0347 REMARK 3 S31: 0.0517 S32: 0.0426 S33: -0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.1800 31.6934 47.4902 REMARK 3 T TENSOR REMARK 3 T11: 0.1659 T22: 0.1420 REMARK 3 T33: 0.1719 T12: -0.0006 REMARK 3 T13: 0.0237 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.0242 L22: 0.0273 REMARK 3 L33: 0.0619 L12: -0.0031 REMARK 3 L13: 0.0292 L23: 0.0375 REMARK 3 S TENSOR REMARK 3 S11: 0.0145 S12: -0.0078 S13: -0.0292 REMARK 3 S21: -0.0603 S22: -0.0918 S23: 0.1107 REMARK 3 S31: 0.0420 S32: 0.0452 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 11 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9686 17.2655 62.6922 REMARK 3 T TENSOR REMARK 3 T11: 0.6895 T22: 0.2853 REMARK 3 T33: 0.1769 T12: 0.0539 REMARK 3 T13: 0.0486 T23: 0.2165 REMARK 3 L TENSOR REMARK 3 L11: 0.0823 L22: 0.1338 REMARK 3 L33: 0.0198 L12: -0.0464 REMARK 3 L13: 0.0022 L23: 0.0011 REMARK 3 S TENSOR REMARK 3 S11: 0.1360 S12: -0.0629 S13: -0.0644 REMARK 3 S21: 0.0507 S22: 0.0988 S23: 0.0202 REMARK 3 S31: 0.0448 S32: 0.0564 S33: 0.1445 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 21 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1662 30.8986 43.4048 REMARK 3 T TENSOR REMARK 3 T11: 0.1372 T22: 0.1002 REMARK 3 T33: 0.1714 T12: 0.0057 REMARK 3 T13: 0.0130 T23: -0.0312 REMARK 3 L TENSOR REMARK 3 L11: 0.0221 L22: 0.0451 REMARK 3 L33: 0.0071 L12: 0.0284 REMARK 3 L13: 0.0112 L23: 0.0136 REMARK 3 S TENSOR REMARK 3 S11: 0.0239 S12: 0.0429 S13: 0.0203 REMARK 3 S21: -0.0081 S22: -0.0204 S23: 0.0700 REMARK 3 S31: -0.0362 S32: 0.0545 S33: -0.0008 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.2003 45.2056 52.0017 REMARK 3 T TENSOR REMARK 3 T11: 0.1273 T22: 0.1954 REMARK 3 T33: 0.1529 T12: 0.0075 REMARK 3 T13: -0.0065 T23: 0.0190 REMARK 3 L TENSOR REMARK 3 L11: 0.0013 L22: 0.0013 REMARK 3 L33: 0.0031 L12: -0.0055 REMARK 3 L13: -0.0021 L23: 0.0029 REMARK 3 S TENSOR REMARK 3 S11: 0.0262 S12: 0.0018 S13: 0.0689 REMARK 3 S21: -0.0102 S22: 0.0362 S23: -0.0243 REMARK 3 S31: -0.0521 S32: 0.0008 S33: -0.0000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 6 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.8010 45.4657 69.1368 REMARK 3 T TENSOR REMARK 3 T11: 0.1308 T22: 0.3133 REMARK 3 T33: 0.1360 T12: 0.0012 REMARK 3 T13: -0.0130 T23: -0.0433 REMARK 3 L TENSOR REMARK 3 L11: 0.0077 L22: 0.0083 REMARK 3 L33: 0.0104 L12: -0.0008 REMARK 3 L13: -0.0079 L23: 0.0071 REMARK 3 S TENSOR REMARK 3 S11: -0.0865 S12: -0.1034 S13: 0.0096 REMARK 3 S21: 0.0400 S22: -0.0526 S23: 0.0416 REMARK 3 S31: -0.0401 S32: -0.0238 S33: -0.0184 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 11 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0158 34.3553 77.1825 REMARK 3 T TENSOR REMARK 3 T11: 0.3222 T22: 0.4124 REMARK 3 T33: 0.2347 T12: -0.0359 REMARK 3 T13: -0.0093 T23: 0.1096 REMARK 3 L TENSOR REMARK 3 L11: 0.0284 L22: 0.0114 REMARK 3 L33: 0.0068 L12: -0.0174 REMARK 3 L13: 0.0113 L23: -0.0055 REMARK 3 S TENSOR REMARK 3 S11: 0.1409 S12: -0.0962 S13: -0.0701 REMARK 3 S21: 0.1777 S22: -0.0008 S23: 0.1125 REMARK 3 S31: 0.1826 S32: -0.0197 S33: 0.0010 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 21 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.8133 47.3840 60.6057 REMARK 3 T TENSOR REMARK 3 T11: 0.1483 T22: 0.1936 REMARK 3 T33: 0.1943 T12: 0.0183 REMARK 3 T13: -0.0123 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.0170 L22: 0.0010 REMARK 3 L33: 0.0233 L12: 0.0047 REMARK 3 L13: -0.0111 L23: 0.0059 REMARK 3 S TENSOR REMARK 3 S11: 0.0404 S12: 0.0322 S13: 0.1109 REMARK 3 S21: 0.0139 S22: -0.0763 S23: 0.0077 REMARK 3 S31: -0.0721 S32: -0.0400 S33: -0.0000 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 31 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.4381 52.4846 51.3929 REMARK 3 T TENSOR REMARK 3 T11: 0.2002 T22: 0.1649 REMARK 3 T33: 0.2145 T12: -0.0166 REMARK 3 T13: -0.0154 T23: 0.0291 REMARK 3 L TENSOR REMARK 3 L11: 0.0010 L22: 0.0017 REMARK 3 L33: 0.0038 L12: 0.0025 REMARK 3 L13: 0.0034 L23: 0.0012 REMARK 3 S TENSOR REMARK 3 S11: 0.0217 S12: 0.0000 S13: 0.0134 REMARK 3 S21: 0.0118 S22: 0.0504 S23: -0.0333 REMARK 3 S31: -0.0022 S32: 0.0075 S33: -0.0000 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 8D5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1000265891. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97648 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46505 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 41.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 1O15 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CALCIUM ACETATE, PEG 3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 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 O HOH A 260 O HOH A 332 1.81 REMARK 500 O HOH A 212 O HOH A 240 1.96 REMARK 500 O HOH D 265 O HOH D 333 1.97 REMARK 500 O HOH A 309 O HOH A 312 1.97 REMARK 500 O HOH B 271 O HOH B 309 1.99 REMARK 500 O HOH A 325 O HOH A 332 2.01 REMARK 500 O HOH C 336 O HOH D 308 2.03 REMARK 500 O HOH C 211 O HOH C 265 2.04 REMARK 500 O HOH A 203 O HOH A 212 2.06 REMARK 500 O HOH A 253 O HOH A 315 2.10 REMARK 500 O HOH C 315 O HOH C 341 2.13 REMARK 500 O HOH C 295 O HOH C 299 2.16 REMARK 500 O HOH A 311 O HOH C 325 2.17 REMARK 500 O HOH B 289 O HOH B 308 2.17 REMARK 500 O HOH A 220 O HOH A 321 2.17 REMARK 500 O HOH A 328 O HOH A 333 2.17 REMARK 500 O HOH A 220 O HOH A 236 2.18 REMARK 500 O HOH D 204 O HOH D 307 2.18 REMARK 500 OP2 C C 9 O HOH C 201 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 304 O HOH B 315 1565 2.03 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 G A 4 O5' - P - OP2 ANGL. DEV. = -5.7 DEGREES REMARK 500 U A 24 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 A B 28 O5' - P - OP1 ANGL. DEV. = -8.6 DEGREES REMARK 500 G C 4 O5' - P - OP2 ANGL. DEV. = -8.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 3 OP1 REMARK 620 2 HOH A 301 O 75.8 REMARK 620 3 G B 2 OP1 109.4 173.4 REMARK 620 4 HOH B 260 O 159.2 86.7 88.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 105 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 8 OP2 REMARK 620 2 C A 9 OP2 99.2 REMARK 620 3 HOH A 260 O 129.3 78.6 REMARK 620 4 HOH A 305 O 71.4 81.1 153.1 REMARK 620 5 HOH A 325 O 117.6 130.4 52.7 139.7 REMARK 620 N 1 2 3 4 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 226 O 95.3 REMARK 620 3 HOH A 227 O 176.5 87.6 REMARK 620 4 HOH A 235 O 91.2 172.9 85.8 REMARK 620 5 HOH A 257 O 92.3 94.1 89.4 88.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 104 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 204 O REMARK 620 2 HOH A 242 O 67.8 REMARK 620 3 HOH A 303 O 76.0 117.8 REMARK 620 4 HOH A 319 O 96.2 60.3 76.2 REMARK 620 5 HOH C 244 O 82.6 87.9 135.6 145.4 REMARK 620 6 HOH C 270 O 85.6 151.1 62.6 137.1 77.5 REMARK 620 7 HOH C 318 O 142.0 127.8 66.1 72.4 127.3 80.1 REMARK 620 8 HOH C 327 O 146.3 83.3 135.3 83.4 79.3 117.4 70.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 104 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 261 O REMARK 620 2 HOH A 263 O 80.8 REMARK 620 3 HOH A 291 O 68.7 90.6 REMARK 620 4 HOH A 307 O 137.2 76.6 75.7 REMARK 620 5 G B 25 OP2 107.5 170.7 88.8 94.3 REMARK 620 6 HOH B 252 O 74.9 108.7 135.2 147.0 78.0 REMARK 620 7 HOH B 270 O 139.6 78.6 145.2 69.7 96.7 79.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 266 O REMARK 620 2 C C 27 O2 75.1 REMARK 620 3 HOH C 243 O 121.7 72.1 REMARK 620 4 HOH C 256 O 138.7 116.1 99.1 REMARK 620 5 HOH C 267 O 76.0 77.5 137.8 68.9 REMARK 620 6 HOH C 321 O 72.6 142.0 143.4 78.3 75.9 REMARK 620 7 HOH C 343 O 141.7 136.9 68.2 56.5 123.8 80.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 4 OP2 REMARK 620 2 U B 23 OP2 171.8 REMARK 620 3 HOH B 237 O 95.6 76.4 REMARK 620 4 HOH B 241 O 96.1 87.5 104.6 REMARK 620 5 HOH B 253 O 95.6 92.0 165.1 83.9 REMARK 620 6 HOH B 291 O 84.8 93.1 86.3 168.8 85.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 105 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 8 OP2 REMARK 620 2 C B 9 OP2 91.6 REMARK 620 3 HOH B 242 O 145.2 68.5 REMARK 620 4 HOH B 307 O 165.5 89.0 47.4 REMARK 620 5 HOH B 312 O 124.2 142.4 74.7 59.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 222 O REMARK 620 2 HOH B 228 O 91.3 REMARK 620 3 HOH B 243 O 90.8 87.9 REMARK 620 4 HOH B 244 O 176.7 91.6 91.0 REMARK 620 5 HOH B 258 O 87.4 174.1 97.9 89.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 104 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C C 3 OP1 REMARK 620 2 G D 2 OP1 108.0 REMARK 620 3 HOH D 267 O 164.0 82.1 REMARK 620 4 HOH D 308 O 83.5 85.5 85.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 219 O REMARK 620 2 HOH C 232 O 172.5 REMARK 620 3 HOH C 251 O 90.3 84.9 REMARK 620 4 HOH C 262 O 94.8 90.8 87.2 REMARK 620 5 HOH C 281 O 93.1 91.4 176.0 94.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 105 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 201 O REMARK 620 2 HOH C 236 O 82.8 REMARK 620 3 HOH C 266 O 86.6 81.2 REMARK 620 4 HOH C 280 O 150.0 72.0 74.0 REMARK 620 5 HOH C 324 O 68.8 147.3 81.2 128.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D 104 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 217 O REMARK 620 2 HOH C 234 O 85.3 REMARK 620 3 HOH C 314 O 136.5 74.6 REMARK 620 4 HOH C 317 O 68.3 86.9 72.3 REMARK 620 5 G D 25 OP2 101.7 168.3 94.0 87.1 REMARK 620 6 HOH D 280 O 79.4 107.4 143.2 143.6 83.2 REMARK 620 7 HOH D 293 O 146.4 80.2 67.7 139.9 98.1 76.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G D 4 OP2 REMARK 620 2 U D 23 OP2 169.2 REMARK 620 3 HOH D 211 O 100.4 69.1 REMARK 620 4 HOH D 228 O 95.6 82.4 91.9 REMARK 620 5 HOH D 262 O 95.3 95.1 164.1 83.8 REMARK 620 6 HOH D 319 O 91.1 93.1 98.2 166.7 84.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 219 O REMARK 620 2 HOH D 234 O 92.0 REMARK 620 3 HOH D 249 O 93.1 174.9 REMARK 620 4 HOH D 261 O 176.0 84.5 90.4 REMARK 620 5 HOH D 269 O 93.4 90.3 90.2 88.6 REMARK 620 N 1 2 3 4 DBREF 8D5L A 1 33 PDB 8D5L 8D5L 1 33 DBREF 8D5L B 1 33 PDB 8D5L 8D5L 1 33 DBREF 8D5L C 1 33 PDB 8D5L 8D5L 1 33 DBREF 8D5L D 1 33 PDB 8D5L 8D5L 1 33 SEQRES 1 A 33 G G C G A U A C C A G C C SEQRES 2 A 33 G A A A G G C C C U U G G SEQRES 3 A 33 C A G C G C C SEQRES 1 B 33 G G C G A U A C C A G C C SEQRES 2 B 33 G A A A G G C C C U U G G SEQRES 3 B 33 C A G C G C C SEQRES 1 C 33 G G C G A U A C C A G C C SEQRES 2 C 33 G A A A G G C C C U U G G SEQRES 3 C 33 C A G C G C C SEQRES 1 D 33 G G C G A U A C C A G C C SEQRES 2 D 33 G A A A G G C C C U U G G SEQRES 3 D 33 C A G C G C C HET QIJ A 101 21 HET MG A 102 1 HET MG A 103 1 HET CA A 104 1 HET NA A 105 1 HET QIJ B 101 21 HET MG B 102 1 HET MG B 103 1 HET CA B 104 1 HET NA B 105 1 HET QIJ C 101 21 HET MG C 102 1 HET CA C 103 1 HET NA C 104 1 HET NA C 105 1 HET QIJ D 101 21 HET MG D 102 1 HET CA D 103 1 HET CA D 104 1 HETNAM QIJ 4-AMINO-8-METHYLPTERIDINE-2,7(1H,8H)-DIONE HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 5 QIJ 4(C7 H7 N5 O2) FORMUL 6 MG 6(MG 2+) FORMUL 8 CA 5(CA 2+) FORMUL 9 NA 4(NA 1+) FORMUL 24 HOH *545(H2 O) LINK OP1 C A 3 MG MG A 103 1555 1555 2.50 LINK OP2 C A 8 NA NA A 105 1555 1555 2.28 LINK OP2 C A 9 NA NA A 105 1555 1555 2.42 LINK MG MG A 102 O HOH A 223 1555 1555 2.04 LINK MG MG A 102 O HOH A 226 1555 1555 2.20 LINK MG MG A 102 O HOH A 227 1555 1555 2.16 LINK MG MG A 102 O HOH A 235 1555 1555 2.19 LINK MG MG A 102 O HOH A 257 1555 1555 2.07 LINK MG MG A 103 O HOH A 301 1555 1555 2.67 LINK MG MG A 103 OP1 G B 2 1555 1555 2.23 LINK MG MG A 103 O HOH B 260 1555 1555 2.40 LINK CA CA A 104 O HOH A 204 1555 1555 2.46 LINK CA CA A 104 O HOH A 242 1555 1555 2.68 LINK CA CA A 104 O HOH A 303 1555 1555 2.64 LINK CA CA A 104 O HOH A 319 1555 1555 2.42 LINK CA CA A 104 O HOH C 244 1555 1555 2.40 LINK CA CA A 104 O HOH C 270 1555 1555 2.50 LINK CA CA A 104 O HOH C 318 1555 1555 2.48 LINK CA CA A 104 O HOH C 327 1555 1555 2.38 LINK NA NA A 105 O HOH A 260 1555 1555 2.02 LINK NA NA A 105 O HOH A 305 1555 1555 3.16 LINK NA NA A 105 O HOH A 325 1555 1555 2.92 LINK O HOH A 261 CA CA B 104 1555 1555 2.32 LINK O HOH A 263 CA CA B 104 1555 1555 2.38 LINK O HOH A 266 CA CA C 103 1655 1555 2.54 LINK O HOH A 291 CA CA B 104 1555 1555 2.69 LINK O HOH A 307 CA CA B 104 1555 1555 2.69 LINK OP2 G B 4 MG MG B 102 1555 1555 2.26 LINK OP2 C B 8 NA NA B 105 1555 1555 2.23 LINK OP2 C B 9 NA NA B 105 1555 1555 2.30 LINK OP2 U B 23 MG MG B 102 1555 1555 2.21 LINK OP2 G B 25 CA CA B 104 1555 1555 2.28 LINK MG MG B 102 O HOH B 237 1555 1555 2.18 LINK MG MG B 102 O HOH B 241 1555 1555 2.15 LINK MG MG B 102 O HOH B 253 1555 1555 2.45 LINK MG MG B 102 O HOH B 291 1555 1555 2.42 LINK MG MG B 103 O HOH B 222 1555 1555 2.09 LINK MG MG B 103 O HOH B 228 1555 1555 2.04 LINK MG MG B 103 O HOH B 243 1555 1555 2.00 LINK MG MG B 103 O HOH B 244 1555 1555 2.09 LINK MG MG B 103 O HOH B 258 1555 1555 2.18 LINK CA CA B 104 O HOH B 252 1555 1555 2.18 LINK CA CA B 104 O HOH B 270 1555 1455 2.46 LINK NA NA B 105 O HOH B 242 1555 1555 2.54 LINK NA NA B 105 O HOH B 307 1555 1555 2.98 LINK NA NA B 105 O HOH B 312 1555 1555 2.17 LINK OP1 C C 3 NA NA C 104 1555 1555 2.51 LINK O2 C C 27 CA CA C 103 1555 1555 2.41 LINK MG MG C 102 O HOH C 219 1555 1555 2.12 LINK MG MG C 102 O HOH C 232 1555 1555 2.14 LINK MG MG C 102 O HOH C 251 1555 1555 2.19 LINK MG MG C 102 O HOH C 262 1555 1555 2.16 LINK MG MG C 102 O HOH C 281 1555 1555 2.09 LINK CA CA C 103 O HOH C 243 1555 1555 2.22 LINK CA CA C 103 O HOH C 256 1555 1555 2.54 LINK CA CA C 103 O HOH C 267 1555 1555 2.27 LINK CA CA C 103 O HOH C 321 1555 1555 2.44 LINK CA CA C 103 O HOH C 343 1555 1555 2.76 LINK NA NA C 104 OP1 G D 2 1555 1555 2.30 LINK NA NA C 104 O HOH D 267 1555 1555 2.48 LINK NA NA C 104 O HOH D 308 1555 1555 2.22 LINK NA NA C 105 O HOH C 201 1555 1555 2.81 LINK NA NA C 105 O HOH C 236 1555 1555 2.61 LINK NA NA C 105 O HOH C 266 1555 1555 2.46 LINK NA NA C 105 O HOH C 280 1555 1555 2.44 LINK NA NA C 105 O HOH C 324 1555 1555 2.29 LINK O HOH C 217 CA CA D 104 1555 1555 2.29 LINK O HOH C 234 CA CA D 104 1555 1555 2.46 LINK O HOH C 314 CA CA D 104 1555 1555 2.60 LINK O HOH C 317 CA CA D 104 1555 1555 2.50 LINK OP2 G D 4 CA CA D 103 1555 1555 2.23 LINK OP2 U D 23 CA CA D 103 1555 1555 2.29 LINK OP2 G D 25 CA CA D 104 1555 1555 2.36 LINK MG MG D 102 O HOH D 219 1555 1555 2.06 LINK MG MG D 102 O HOH D 234 1555 1555 2.25 LINK MG MG D 102 O HOH D 249 1555 1555 2.12 LINK MG MG D 102 O HOH D 261 1555 1555 2.18 LINK MG MG D 102 O HOH D 269 1555 1555 1.97 LINK CA CA D 103 O HOH D 211 1555 1555 2.22 LINK CA CA D 103 O HOH D 228 1555 1555 2.43 LINK CA CA D 103 O HOH D 262 1555 1555 2.37 LINK CA CA D 103 O HOH D 319 1555 1555 2.41 LINK CA CA D 104 O HOH D 280 1555 1555 2.36 LINK CA CA D 104 O HOH D 293 1555 1455 2.47 CRYST1 25.606 50.271 79.845 94.28 91.53 90.13 P 1 4 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 0.039053 0.000089 0.001053 0.00000 SCALE2 0.000000 0.019892 0.001490 0.00000 SCALE3 0.000000 0.000000 0.012564 0.00000