HEADER TRANSFERASE/RNA 15-NOV-18 6IS0 TITLE CRYSTAL STRUCTURE OF THE ZEBRAFISH CAP-SPECIFIC ADENOSINE TITLE 2 METHYLTRANSFERASE BOUND TO SAH AND M7G-CAPPED RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PDX1 C-TERMINAL-INHIBITING FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: M7G-CAPPED RNA; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: PCIF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PE-SUMO; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS RNA METHYLATION, METHYLTRANSFERASE, M6A, N6-METHYLADENOSINE, KEYWDS 2 TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.HIRANO,H.NISHIMASU,R.ISHITANI,O.NUREKI REVDAT 5 06-MAR-24 6IS0 1 COMPND FORMUL REVDAT 4 22-NOV-23 6IS0 1 REMARK REVDAT 3 28-OCT-20 6IS0 1 JRNL REVDAT 2 23-JAN-19 6IS0 1 JRNL REVDAT 1 05-DEC-18 6IS0 0 JRNL AUTH S.AKICHIKA,S.HIRANO,Y.SHICHINO,T.SUZUKI,H.NISHIMASU, JRNL AUTH 2 R.ISHITANI,A.SUGITA,Y.HIROSE,S.IWASAKI,O.NUREKI,T.SUZUKI JRNL TITL CAP-SPECIFIC TERMINAL N 6 -METHYLATION OF RNA BY AN RNA JRNL TITL 2 POLYMERASE II-ASSOCIATED METHYLTRANSFERASE. JRNL REF SCIENCE V. 363 2019 JRNL REFN ESSN 1095-9203 JRNL PMID 30467178 JRNL DOI 10.1126/SCIENCE.AAV0080 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 53942 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 2657 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 47.7529 - 4.8016 1.00 2923 161 0.1851 0.2047 REMARK 3 2 4.8016 - 3.8117 1.00 2780 154 0.1542 0.1931 REMARK 3 3 3.8117 - 3.3300 1.00 2775 140 0.1731 0.2331 REMARK 3 4 3.3300 - 3.0256 1.00 2747 138 0.1815 0.2115 REMARK 3 5 3.0256 - 2.8088 0.99 2719 138 0.1849 0.2357 REMARK 3 6 2.8088 - 2.6432 0.99 2700 142 0.1846 0.2283 REMARK 3 7 2.6432 - 2.5108 0.99 2695 156 0.1753 0.2035 REMARK 3 8 2.5108 - 2.4015 0.99 2685 145 0.1718 0.2139 REMARK 3 9 2.4015 - 2.3091 0.99 2692 136 0.1774 0.2091 REMARK 3 10 2.3091 - 2.2294 0.99 2707 137 0.1706 0.2106 REMARK 3 11 2.2294 - 2.1597 0.99 2649 117 0.1747 0.2199 REMARK 3 12 2.1597 - 2.0979 0.98 2699 140 0.1738 0.1816 REMARK 3 13 2.0979 - 2.0427 0.99 2646 142 0.1811 0.2340 REMARK 3 14 2.0427 - 1.9929 0.99 2672 118 0.1787 0.2178 REMARK 3 15 1.9929 - 1.9476 0.98 2657 141 0.1890 0.2322 REMARK 3 16 1.9476 - 1.9061 0.98 2615 136 0.2003 0.2244 REMARK 3 17 1.9061 - 1.8680 0.98 2618 154 0.2042 0.2574 REMARK 3 18 1.8680 - 1.8327 0.98 2675 134 0.2148 0.2568 REMARK 3 19 1.8327 - 1.8000 0.98 2631 128 0.2328 0.2841 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.45 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 : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 178 THROUGH 202 ) REMARK 3 ORIGIN FOR THE GROUP (A): 68.1091 13.7927 4.6215 REMARK 3 T TENSOR REMARK 3 T11: 0.2535 T22: 0.3137 REMARK 3 T33: 0.2831 T12: 0.0053 REMARK 3 T13: 0.0033 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 0.7330 L22: 2.7317 REMARK 3 L33: 0.9767 L12: 0.1604 REMARK 3 L13: -0.8251 L23: -0.3496 REMARK 3 S TENSOR REMARK 3 S11: 0.1453 S12: -0.0002 S13: 0.1232 REMARK 3 S21: -0.1688 S22: -0.1392 S23: -0.2167 REMARK 3 S31: -0.1746 S32: 0.2187 S33: -0.0186 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 203 THROUGH 274 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.3370 6.0862 23.8386 REMARK 3 T TENSOR REMARK 3 T11: 0.2168 T22: 0.2585 REMARK 3 T33: 0.1881 T12: 0.0436 REMARK 3 T13: 0.0080 T23: 0.0240 REMARK 3 L TENSOR REMARK 3 L11: 2.2231 L22: 1.5289 REMARK 3 L33: 2.6225 L12: -0.5099 REMARK 3 L13: -1.9441 L23: 1.3055 REMARK 3 S TENSOR REMARK 3 S11: -0.0371 S12: -0.0641 S13: -0.0125 REMARK 3 S21: 0.1461 S22: -0.0338 S23: 0.1152 REMARK 3 S31: 0.0696 S32: -0.0922 S33: 0.0638 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 275 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.8876 15.0235 28.4802 REMARK 3 T TENSOR REMARK 3 T11: 0.4714 T22: 0.5210 REMARK 3 T33: 0.3621 T12: 0.1659 REMARK 3 T13: 0.0350 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 3.5351 L22: 3.5594 REMARK 3 L33: 3.1768 L12: -0.6280 REMARK 3 L13: -0.2476 L23: -0.5877 REMARK 3 S TENSOR REMARK 3 S11: 0.0396 S12: 0.6005 S13: -0.5051 REMARK 3 S21: -0.8484 S22: -0.2134 S23: 0.4986 REMARK 3 S31: -0.0751 S32: -0.8430 S33: 0.1437 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 306 THROUGH 334 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.6895 19.9313 38.9600 REMARK 3 T TENSOR REMARK 3 T11: 0.5099 T22: 0.5511 REMARK 3 T33: 0.4529 T12: 0.1975 REMARK 3 T13: 0.0779 T23: -0.0484 REMARK 3 L TENSOR REMARK 3 L11: 4.0790 L22: 3.1167 REMARK 3 L33: 1.5205 L12: -1.0590 REMARK 3 L13: 0.1270 L23: -0.8229 REMARK 3 S TENSOR REMARK 3 S11: -0.2395 S12: -0.2728 S13: 0.1282 REMARK 3 S21: 0.2979 S22: 0.2399 S23: 0.6310 REMARK 3 S31: -0.4530 S32: -0.7757 S33: 0.1054 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 335 THROUGH 389 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.0724 8.9869 28.5191 REMARK 3 T TENSOR REMARK 3 T11: 0.3703 T22: 0.2380 REMARK 3 T33: 0.2592 T12: 0.0347 REMARK 3 T13: 0.0024 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 1.3227 L22: 0.2832 REMARK 3 L33: 2.2427 L12: -0.1655 REMARK 3 L13: -1.2945 L23: 0.8541 REMARK 3 S TENSOR REMARK 3 S11: 0.0687 S12: -0.2633 S13: -0.0592 REMARK 3 S21: -0.0992 S22: -0.0890 S23: 0.1599 REMARK 3 S31: -0.2573 S32: 0.0533 S33: 0.0551 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 390 THROUGH 423 ) REMARK 3 ORIGIN FOR THE GROUP (A): 75.1301 4.6507 8.9885 REMARK 3 T TENSOR REMARK 3 T11: 0.2143 T22: 0.3568 REMARK 3 T33: 0.3257 T12: 0.0387 REMARK 3 T13: -0.0422 T23: 0.0394 REMARK 3 L TENSOR REMARK 3 L11: 1.1042 L22: 3.5910 REMARK 3 L33: 1.5583 L12: 0.7481 REMARK 3 L13: -1.1463 L23: -0.2426 REMARK 3 S TENSOR REMARK 3 S11: 0.0911 S12: -0.2682 S13: 0.0247 REMARK 3 S21: 0.2519 S22: -0.1062 S23: -0.4192 REMARK 3 S31: -0.0323 S32: 0.5188 S33: 0.0019 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 424 THROUGH 459 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.2893 0.6995 -3.6783 REMARK 3 T TENSOR REMARK 3 T11: 0.2660 T22: 0.2987 REMARK 3 T33: 0.2224 T12: 0.0327 REMARK 3 T13: -0.0351 T23: -0.0369 REMARK 3 L TENSOR REMARK 3 L11: 3.0902 L22: 2.8256 REMARK 3 L33: 3.6199 L12: -0.2555 REMARK 3 L13: 0.8917 L23: 0.2548 REMARK 3 S TENSOR REMARK 3 S11: 0.0976 S12: 0.4651 S13: -0.2358 REMARK 3 S21: -0.4839 S22: -0.0553 S23: 0.2832 REMARK 3 S31: 0.1857 S32: -0.4159 S33: -0.0104 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 460 THROUGH 484 ) REMARK 3 ORIGIN FOR THE GROUP (A): 61.4304 1.0729 3.1576 REMARK 3 T TENSOR REMARK 3 T11: 0.1944 T22: 0.2208 REMARK 3 T33: 0.2048 T12: 0.0320 REMARK 3 T13: -0.0108 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.8033 L22: 1.8398 REMARK 3 L33: 2.3401 L12: 0.7867 REMARK 3 L13: -0.8090 L23: -0.3480 REMARK 3 S TENSOR REMARK 3 S11: 0.1074 S12: 0.0533 S13: 0.0772 REMARK 3 S21: 0.0706 S22: -0.1082 S23: 0.0453 REMARK 3 S31: -0.0796 S32: -0.0618 S33: 0.0018 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 485 THROUGH 532 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.5605 21.1628 2.4404 REMARK 3 T TENSOR REMARK 3 T11: 0.3300 T22: 0.2557 REMARK 3 T33: 0.2788 T12: 0.0444 REMARK 3 T13: -0.0142 T23: 0.0172 REMARK 3 L TENSOR REMARK 3 L11: 1.3283 L22: 1.9288 REMARK 3 L33: 2.3432 L12: -0.9715 REMARK 3 L13: 0.1424 L23: 0.4256 REMARK 3 S TENSOR REMARK 3 S11: 0.1611 S12: 0.1427 S13: 0.1732 REMARK 3 S21: -0.3977 S22: -0.1445 S23: 0.1605 REMARK 3 S31: -0.3967 S32: -0.0015 S33: -0.0292 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 533 THROUGH 605 ) REMARK 3 ORIGIN FOR THE GROUP (A): 60.0276 24.3190 14.7414 REMARK 3 T TENSOR REMARK 3 T11: 0.2882 T22: 0.2168 REMARK 3 T33: 0.2686 T12: 0.0144 REMARK 3 T13: 0.0010 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.8636 L22: 2.4597 REMARK 3 L33: 2.6350 L12: -0.0748 REMARK 3 L13: -0.4100 L23: 0.4705 REMARK 3 S TENSOR REMARK 3 S11: 0.0703 S12: -0.1674 S13: 0.3887 REMARK 3 S21: 0.1036 S22: 0.0182 S23: 0.0538 REMARK 3 S31: -0.4837 S32: 0.0539 S33: -0.0824 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 606 THROUGH 673 ) REMARK 3 ORIGIN FOR THE GROUP (A): 54.9551 34.1560 5.4565 REMARK 3 T TENSOR REMARK 3 T11: 0.6335 T22: 0.3025 REMARK 3 T33: 0.5737 T12: 0.0888 REMARK 3 T13: 0.0291 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 2.6959 L22: 1.8624 REMARK 3 L33: 2.7623 L12: -0.9694 REMARK 3 L13: 0.0458 L23: 0.8028 REMARK 3 S TENSOR REMARK 3 S11: 0.1859 S12: 0.2936 S13: 0.4114 REMARK 3 S21: -0.4043 S22: -0.1694 S23: 0.3519 REMARK 3 S31: -0.7018 S32: -0.4182 S33: -0.0417 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 6IS0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009795. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54004 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 47.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.57600 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: MOLREP REMARK 200 STARTING MODEL: 6IRX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG 3350, 0.1M POTASSIUM REMARK 280 THIOCYANATE, 0.05M BIS-TRIS PROPANE, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 37.10950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.48500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.01750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.48500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.10950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.01750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 2510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 KCAL/MOL 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 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -37.10950 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 42.01750 REMARK 350 BIOMT3 2 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 THR A 397 REMARK 465 GLU A 398 REMARK 465 SER A 399 REMARK 465 ALA A 400 REMARK 465 GLY A 487 REMARK 465 VAL A 488 REMARK 465 ASN A 489 REMARK 465 GLU A 490 REMARK 465 GLY A 491 REMARK 465 SER A 492 REMARK 465 GLY A 493 REMARK 465 LEU A 494 REMARK 465 GLN A 495 REMARK 465 GLY A 626 REMARK 465 SER A 627 REMARK 465 GLN A 628 REMARK 465 HIS A 629 REMARK 465 ILE A 630 REMARK 465 CYS A 631 REMARK 465 LYS A 632 REMARK 465 ARG A 633 REMARK 465 GLU A 634 REMARK 465 GLU A 635 REMARK 465 ILE A 636 REMARK 465 TYR A 637 REMARK 465 TYR A 638 REMARK 465 LYS A 639 REMARK 465 ALA A 640 REMARK 465 ILE A 641 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 ARG A 281 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 284 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 328 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 257 -8.65 -155.12 REMARK 500 ASP A 463 61.30 -152.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1110 DISTANCE = 5.81 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAH A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue M7G A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B3P A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues M7G C 1 and A2M C 2 DBREF1 6IS0 A 178 673 UNP A0A0R4IKJ1_DANRE DBREF2 6IS0 A A0A0R4IKJ1 178 673 DBREF 6IS0 C 1 3 PDB 6IS0 6IS0 1 3 SEQADV 6IS0 VAL A 308 UNP A0A0R4IKJ ALA 308 ENGINEERED MUTATION SEQADV 6IS0 ASN A 344 UNP A0A0R4IKJ HIS 344 ENGINEERED MUTATION SEQRES 1 A 496 VAL TYR TRP ASP LEU ASP ILE GLN THR ASN ALA VAL ILE SEQRES 2 A 496 ARG GLU ARG ALA PRO ALA ASP HIS LEU PRO PRO HIS PRO SEQRES 3 A 496 GLU ILE GLU LEU GLN ARG ALA GLN LEU THR THR LYS LEU SEQRES 4 A 496 ARG GLN HIS TYR HIS GLU LEU CYS SER GLN ARG GLU GLY SEQRES 5 A 496 ILE GLU PRO PRO ARG GLU SER PHE ASN ARG TRP LEU LEU SEQRES 6 A 496 GLU ARG LYS VAL VAL ASP LYS GLY LEU ASP PRO LEU LEU SEQRES 7 A 496 PRO SER GLU CYS ASP PRO VAL ILE SER PRO SER MET PHE SEQRES 8 A 496 ARG GLU ILE MET ASN ASP ILE PRO ILE ARG LEU SER ARG SEQRES 9 A 496 ILE LYS TYR LYS GLU GLU ALA ARG LYS LEU LEU PHE LYS SEQRES 10 A 496 TYR ALA GLU ALA ALA LYS LYS MET ILE ASP SER ARG ASN SEQRES 11 A 496 VAL THR PRO GLU SER ARG LYS VAL VAL LYS TRP ASN VAL SEQRES 12 A 496 GLU ASP THR MET ASN TRP LEU ARG ARG ASP HIS SER ALA SEQRES 13 A 496 SER LYS GLU ASP TYR MET ASP ARG LEU GLU ASN LEU ARG SEQRES 14 A 496 LYS GLN CYS GLY PRO HIS VAL ALA SER VAL ALA LYS ASP SEQRES 15 A 496 SER VAL GLU GLY ILE CYS SER LYS ILE TYR HIS ILE SER SEQRES 16 A 496 ALA GLU TYR VAL ARG ARG ILE ARG GLN ALA HIS LEU THR SEQRES 17 A 496 LEU LEU LYS GLU CYS ASN ILE SER VAL ASP GLY THR GLU SEQRES 18 A 496 SER ALA GLU VAL GLN ASP ARG LEU VAL TYR CYS TYR PRO SEQRES 19 A 496 VAL ARG LEU SER ILE PRO ALA PRO PRO GLN THR ARG VAL SEQRES 20 A 496 GLU LEU HIS PHE GLU ASN ASP ILE ALA CYS LEU ARG PHE SEQRES 21 A 496 LYS GLY GLU MET VAL LYS VAL SER ARG GLY HIS PHE ASN SEQRES 22 A 496 LYS LEU GLU LEU LEU TYR ARG TYR SER CYS ILE ASP ASP SEQRES 23 A 496 PRO ARG PHE GLU LYS PHE LEU SER ARG VAL TRP CYS LEU SEQRES 24 A 496 ILE LYS ARG TYR GLN VAL MET PHE GLY SER GLY VAL ASN SEQRES 25 A 496 GLU GLY SER GLY LEU GLN GLY SER LEU PRO VAL PRO VAL SEQRES 26 A 496 PHE GLU ALA LEU ASN LYS GLN PHE GLY VAL THR PHE GLU SEQRES 27 A 496 CYS PHE ALA SER PRO LEU ASN CYS TYR PHE LYS GLN PHE SEQRES 28 A 496 CYS SER ALA PHE PRO ASP ILE ASP GLY PHE PHE GLY SER SEQRES 29 A 496 ARG GLY PRO PHE LEU SER PHE SER PRO ALA SER GLY SER SEQRES 30 A 496 PHE GLU ALA ASN PRO PRO PHE CYS GLU GLU LEU MET ASP SEQRES 31 A 496 ALA MET VAL THR HIS PHE GLU ASP LEU LEU GLY ARG SER SEQRES 32 A 496 SER GLU PRO LEU SER PHE ILE ILE PHE VAL PRO GLU TRP SEQRES 33 A 496 ARG ASP PRO PRO THR PRO ALA LEU THR ARG MET GLU ALA SEQRES 34 A 496 SER ARG PHE ARG ARG HIS GLN MET THR VAL PRO ALA PHE SEQRES 35 A 496 GLU HIS GLU TYR ARG SER GLY SER GLN HIS ILE CYS LYS SEQRES 36 A 496 ARG GLU GLU ILE TYR TYR LYS ALA ILE HIS GLY THR ALA SEQRES 37 A 496 VAL ILE PHE LEU GLN ASN ASN ALA GLY PHE ALA LYS TRP SEQRES 38 A 496 GLU PRO THR THR GLU ARG ILE GLN GLU LEU LEU ALA ALA SEQRES 39 A 496 TYR LYS SEQRES 1 C 3 M7G A2M G HET M7G C 1 29 HET A2M C 2 23 HET SAH A 701 26 HET M7G A 702 29 HET EDO A 703 4 HET EDO A 704 4 HET EDO A 705 4 HET EDO A 706 4 HET B3P A 707 19 HETNAM M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE HETNAM A2M 2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM EDO 1,2-ETHANEDIOL HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- HETNAM 2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 M7G 2(C11 H18 N5 O11 P2 1+) FORMUL 2 A2M C11 H16 N5 O7 P FORMUL 3 SAH C14 H20 N6 O5 S FORMUL 5 EDO 4(C2 H6 O2) FORMUL 9 B3P C11 H26 N2 O6 FORMUL 10 HOH *313(H2 O) HELIX 1 AA1 HIS A 202 GLY A 229 1 28 HELIX 2 AA2 GLU A 235 ASP A 248 1 14 HELIX 3 AA3 SER A 264 ASP A 274 1 11 HELIX 4 AA4 TYR A 284 ARG A 306 1 23 HELIX 5 AA5 THR A 309 ARG A 329 1 21 HELIX 6 AA6 SER A 334 CYS A 390 1 57 HELIX 7 AA7 ARG A 446 CYS A 460 1 15 HELIX 8 AA8 LYS A 468 GLY A 485 1 18 HELIX 9 AA9 PRO A 499 GLY A 511 1 13 HELIX 10 AB1 PHE A 532 GLY A 537 1 6 HELIX 11 AB2 PHE A 538 GLY A 540 5 3 HELIX 12 AB3 PRO A 544 PHE A 548 5 5 HELIX 13 AB4 CYS A 562 SER A 580 1 19 HELIX 14 AB5 THR A 598 ALA A 606 1 9 HELIX 15 AB6 ASN A 651 TRP A 658 1 8 HELIX 16 AB7 THR A 661 TYR A 672 1 12 SHEET 1 AA1 4 LEU A 406 TYR A 408 0 SHEET 2 AA1 4 VAL A 189 ARG A 191 -1 N ILE A 190 O VAL A 407 SHEET 3 AA1 4 PRO A 550 ALA A 557 -1 O ALA A 551 N VAL A 189 SHEET 4 AA1 4 PHE A 514 GLU A 515 1 N PHE A 514 O GLU A 556 SHEET 1 AA2 6 LEU A 406 TYR A 408 0 SHEET 2 AA2 6 VAL A 189 ARG A 191 -1 N ILE A 190 O VAL A 407 SHEET 3 AA2 6 PRO A 550 ALA A 557 -1 O ALA A 551 N VAL A 189 SHEET 4 AA2 6 LEU A 584 PRO A 591 1 O SER A 585 N PHE A 555 SHEET 5 AA2 6 THR A 644 GLN A 650 -1 O LEU A 649 N PHE A 586 SHEET 6 AA2 6 ARG A 610 VAL A 616 -1 N MET A 614 O VAL A 646 SHEET 1 AA3 3 GLU A 425 GLU A 429 0 SHEET 2 AA3 3 ILE A 432 PHE A 437 -1 O CYS A 434 N HIS A 427 SHEET 3 AA3 3 GLU A 440 SER A 445 -1 O VAL A 444 N ALA A 433 LINK O1B M7G C 1 P A2M C 2 1555 1555 1.61 LINK O3' A2M C 2 P G C 3 1555 1555 1.61 CISPEP 1 ASP A 260 PRO A 261 0 5.96 CISPEP 2 ILE A 275 PRO A 276 0 2.60 CISPEP 3 ASP A 595 PRO A 596 0 1.90 SITE 1 AC1 21 SER A 497 LEU A 498 PHE A 503 GLU A 515 SITE 2 AC1 21 CYS A 516 PHE A 517 ALA A 518 SER A 519 SITE 3 AC1 21 ASN A 522 CYS A 529 SER A 530 PRO A 544 SITE 4 AC1 21 PHE A 545 GLU A 556 ASN A 558 PRO A 560 SITE 5 AC1 21 EDO A 706 HOH A 809 HOH A 846 HOH A 918 SITE 6 AC1 21 HOH A1030 SITE 1 AC2 12 ARG A 239 ARG A 269 GLU A 563 TRP A 593 SITE 2 AC2 12 ASP A 595 PRO A 596 PRO A 597 THR A 598 SITE 3 AC2 12 HOH A 839 HOH A 877 HOH A 926 HOH A 953 SITE 1 AC3 6 HIS A 198 LEU A 251 PRO A 253 HOH A 841 SITE 2 AC3 6 HOH A 891 HOH A 917 SITE 1 AC4 8 LEU A 241 LYS A 245 PRO A 253 LEU A 254 SITE 2 AC4 8 ALA A 531 PHE A 532 HOH A 809 HOH A 909 SITE 1 AC5 8 PRO A 201 HIS A 202 PRO A 203 PRO A 419 SITE 2 AC5 8 PRO A 420 LYS A 468 SER A 471 HOH A 939 SITE 1 AC6 7 ASN A 558 PRO A 559 PRO A 560 PHE A 561 SITE 2 AC6 7 SAH A 701 HOH A 820 HOH A 836 SITE 1 AC7 15 GLU A 192 ARG A 193 ALA A 194 PRO A 195 SITE 2 AC7 15 GLU A 401 VAL A 402 GLN A 403 ASP A 404 SITE 3 AC7 15 ARG A 405 TYR A 410 PRO A 501 GLU A 504 SITE 4 AC7 15 GLU A 620 HOH A 827 HOH A 857 SITE 1 AC8 20 VAL A 178 TYR A 179 ARG A 191 LYS A 285 SITE 2 AC8 20 SER A 334 LYS A 335 GLU A 374 ARG A 377 SITE 3 AC8 20 ARG A 378 ASP A 404 ARG A 405 LEU A 406 SITE 4 AC8 20 ASP A 431 ARG A 446 VAL A 500 GLU A 622 SITE 5 AC8 20 TYR A 623 ARG A 624 G C 3 HOH C 101 CRYST1 74.219 84.035 92.970 90.00 90.00 90.00 P 21 21 21 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 0.013474 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011900 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010756 0.00000