HEADER RNA 17-MAR-14 4P5J TITLE CRYSTAL STRUCTURE OF THE TRNA-LIKE STRUCTURE FROM TURNIP YELLOW MOSAIC TITLE 2 VIRUS (TYMV), A TRNA MIMICKING RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TURNIP YELLOW MOSAIC VIRUS MRNA FOR THE COAT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: TURNIP YELLOW MOSAIC VIRUS; SOURCE 4 ORGANISM_TAXID: 12154; SOURCE 5 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 6 RNA POLYMERASE KEYWDS TRNA-MIMIC VIRAL RNA PSEUDOKNOT MULTIFUNCTIONAL, RNA EXPDTA X-RAY DIFFRACTION AUTHOR T.M.COLUSSI,D.A.COSTANTINO,J.A.HAMMOND,G.M.RUEHLE,J.C.NIX,J.S.KIEFT REVDAT 7 27-DEC-23 4P5J 1 REMARK LINK REVDAT 6 20-NOV-19 4P5J 1 REMARK REVDAT 5 06-SEP-17 4P5J 1 SOURCE JRNL REMARK REVDAT 4 01-OCT-14 4P5J 1 JRNL REVDAT 3 30-JUL-14 4P5J 1 JRNL REVDAT 2 25-JUN-14 4P5J 1 JRNL REVDAT 1 04-JUN-14 4P5J 0 JRNL AUTH T.M.COLUSSI,D.A.COSTANTINO,J.A.HAMMOND,G.M.RUEHLE,J.C.NIX, JRNL AUTH 2 J.S.KIEFT JRNL TITL THE STRUCTURAL BASIS OF TRANSFER RNA MIMICRY AND JRNL TITL 2 CONFORMATIONAL PLASTICITY BY A VIRAL RNA. JRNL REF NATURE V. 511 366 2014 JRNL REFN ESSN 1476-4687 JRNL PMID 24909993 JRNL DOI 10.1038/NATURE13378 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.HAMMOND,R.P.RAMBO,J.S.KIEFT REMARK 1 TITL MULTI-DOMAIN PACKING IN THE AMINOACYLATABLE 3' END OF A REMARK 1 TITL 2 PLANT VIRAL RNA. REMARK 1 REF J.MOL.BIOL. V. 399 450 2010 REMARK 1 REFN ESSN 1089-8638 REMARK 1 PMID 20398674 REMARK 1 DOI 10.1016/J.JMB.2010.04.016 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.A.HAMMOND,R.P.RAMBO,M.E.FILBIN,J.S.KIEFT REMARK 1 TITL COMPARISON AND FUNCTIONAL IMPLICATIONS OF THE 3D REMARK 1 TITL 2 ARCHITECTURES OF VIRAL TRNA-LIKE STRUCTURES. REMARK 1 REF RNA V. 15 294 2009 REMARK 1 REFN ESSN 1469-9001 REMARK 1 PMID 19144910 REMARK 1 DOI 10.1261/RNA.1360709 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 41334 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.170 REMARK 3 FREE R VALUE TEST SET COUNT : 3790 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 28.8736 - 5.9568 0.98 1392 138 0.2029 0.2058 REMARK 3 2 5.9568 - 4.7349 1.00 1392 138 0.1556 0.2057 REMARK 3 3 4.7349 - 4.1383 1.00 1387 144 0.1695 0.1714 REMARK 3 4 4.1383 - 3.7608 1.00 1421 143 0.1764 0.2050 REMARK 3 5 3.7608 - 3.4918 1.00 1369 139 0.1743 0.1896 REMARK 3 6 3.4918 - 3.2862 1.00 1413 141 0.1804 0.2382 REMARK 3 7 3.2862 - 3.1218 1.00 1403 136 0.1825 0.2412 REMARK 3 8 3.1218 - 2.9861 1.00 1404 143 0.2053 0.2124 REMARK 3 9 2.9861 - 2.8712 1.00 1391 133 0.2373 0.3721 REMARK 3 10 2.8712 - 2.7722 1.00 1395 142 0.2741 0.2994 REMARK 3 11 2.7722 - 2.6856 1.00 1400 147 0.2557 0.2850 REMARK 3 12 2.6856 - 2.6089 1.00 1404 143 0.2521 0.2989 REMARK 3 13 2.6089 - 2.5403 1.00 1396 142 0.2497 0.2752 REMARK 3 14 2.5403 - 2.4783 1.00 1396 143 0.2501 0.3312 REMARK 3 15 2.4783 - 2.4220 1.00 1377 141 0.2295 0.2489 REMARK 3 16 2.4220 - 2.3705 1.00 1419 142 0.2279 0.2770 REMARK 3 17 2.3705 - 2.3231 1.00 1413 143 0.2316 0.2825 REMARK 3 18 2.3231 - 2.2793 1.00 1363 138 0.2262 0.2641 REMARK 3 19 2.2793 - 2.2386 1.00 1401 143 0.2277 0.2925 REMARK 3 20 2.2386 - 2.2007 1.00 1410 143 0.2346 0.2812 REMARK 3 21 2.2007 - 2.1652 1.00 1388 139 0.2360 0.2496 REMARK 3 22 2.1652 - 2.1319 1.00 1396 140 0.2567 0.2982 REMARK 3 23 2.1319 - 2.1005 1.00 1391 140 0.2746 0.2785 REMARK 3 24 2.1005 - 2.0709 1.00 1379 136 0.2830 0.3230 REMARK 3 25 2.0709 - 2.0430 1.00 1410 148 0.2883 0.3024 REMARK 3 26 2.0430 - 2.0164 1.00 1395 139 0.2973 0.3908 REMARK 3 27 2.0164 - 1.9912 0.90 1239 126 0.3046 0.3259 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.011 2078 REMARK 3 ANGLE : 1.791 3295 REMARK 3 CHIRALITY : 0.082 420 REMARK 3 PLANARITY : 0.013 84 REMARK 3 DIHEDRAL : 14.148 1042 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 4P5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000200737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-13 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 : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0972 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK SI(111) SAGITALLY REMARK 200 FOCUSED MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41343 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 66.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.450 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.82000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.190 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THIS RNA WAS PREPARED FOR REMARK 280 CRYSTALLOGRAPHY IN A SOLUTION CONTAINING 5 MG/ML RNA, 2.5 MM REMARK 280 MGCL2, AND 10 MM HEPES-KOH PH 7.5. THIS MIXTURE WAS HEATED TO 65? REMARK 280 C FOR 3 MINUTES, THEN COOLED AT ROOM TEMPERATURE. AFTER COOLING, REMARK 280 SPERMIDINE WAS ADDED TO 0.5 MM. THE REACTION WAS CENTRIFUGED FOR REMARK 280 10 MINUTES AT 13000 X G AND THEN USED IN SITTING-DROP VAPOR REMARK 280 DIFFUSION CRYSTALLIZATION AT 4?C. 1 ?L OF RNA SOLUTION WAS REMARK 280 COMBINED WITH 2 ?L OF 10% MPD, 40 MM NA-CACODYLATE PH 6.0, 12 MM REMARK 280 SPERMINE, 80 MM NACL, AND 20 MM MGCL2. THE WELL SOLUTION WAS 20- REMARK 280 35% MPD. CRYSTALS APPEARED AND GREW TO FULL SIZE OVER THE COURSE REMARK 280 OF 1-2 DAYS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.63500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.78500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 55.80500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.63500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.78500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.80500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.63500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.78500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.80500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.63500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.78500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.80500 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 TOTAL BURIED SURFACE AREA: 4020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 219 LIES ON A SPECIAL POSITION. 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 U A -1 REMARK 465 U A 0 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 O6 G A 23 O HOH A 324 2.14 REMARK 500 O2 U A 26 N3 IRI A 104 2.17 REMARK 500 N1 IRI A 104 O HOH A 311 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 A A 51 N3 A A 51 C4 0.036 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 C A 5 N3 - C4 - N4 ANGL. DEV. = -4.5 DEGREES REMARK 500 A A 9 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 G A 10 C4 - C5 - N7 ANGL. DEV. = -2.8 DEGREES REMARK 500 U A 12 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 14 C8 - N9 - C4 ANGL. DEV. = 2.9 DEGREES REMARK 500 G A 16 N7 - C8 - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 G A 16 C8 - N9 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 G A 16 N1 - C6 - O6 ANGL. DEV. = 4.2 DEGREES REMARK 500 G A 16 C5 - C6 - O6 ANGL. DEV. = -4.6 DEGREES REMARK 500 G A 23 C5 - C6 - O6 ANGL. DEV. = -4.7 DEGREES REMARK 500 U A 42 O5' - P - OP2 ANGL. DEV. = -6.0 DEGREES REMARK 500 U A 42 C2 - N3 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 G A 48 OP1 - P - OP2 ANGL. DEV. = 9.0 DEGREES REMARK 500 G A 48 C2 - N3 - C4 ANGL. DEV. = 5.0 DEGREES REMARK 500 G A 48 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 A A 50 C2 - N3 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 50 N1 - C6 - N6 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 51 C8 - N9 - C4 ANGL. DEV. = 2.9 DEGREES REMARK 500 C A 52 O3' - P - OP1 ANGL. DEV. = 6.9 DEGREES REMARK 500 C A 59 O3' - P - OP2 ANGL. DEV. = 6.8 DEGREES REMARK 500 C A 60 N1 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 U A 62 O5' - P - OP2 ANGL. DEV. = -6.4 DEGREES REMARK 500 C A 63 N3 - C4 - N4 ANGL. DEV. = -4.9 DEGREES REMARK 500 G A 70 O5' - P - OP2 ANGL. DEV. = -11.0 DEGREES REMARK 500 G A 71 O5' - P - OP1 ANGL. DEV. = -6.6 DEGREES REMARK 500 G A 71 N1 - C6 - O6 ANGL. DEV. = 4.2 DEGREES REMARK 500 G A 71 C5 - C6 - O6 ANGL. DEV. = -4.6 DEGREES REMARK 500 A A 75 C6 - N1 - C2 ANGL. DEV. = 4.4 DEGREES REMARK 500 A A 75 N1 - C2 - N3 ANGL. DEV. = -3.4 DEGREES REMARK 500 U A 76 C6 - N1 - C2 ANGL. DEV. = 3.6 DEGREES REMARK 500 C A 77 C5' - C4' - O4' ANGL. DEV. = 6.2 DEGREES REMARK 500 A23 A 84 O3' - P - OP2 ANGL. DEV. = 16.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G A 48 0.05 SIDE CHAIN 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 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 40 OP2 REMARK 620 2 HOH A 225 O 90.7 REMARK 620 3 HOH A 228 O 80.8 78.2 REMARK 620 4 HOH A 244 O 81.3 152.8 74.9 REMARK 620 5 HOH A 252 O 156.8 76.7 77.6 101.0 REMARK 620 6 HOH A 273 O 111.7 90.7 163.6 116.4 88.2 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 224 O REMARK 620 2 HOH A 226 O 88.2 REMARK 620 3 HOH A 227 O 88.8 174.8 REMARK 620 4 HOH A 229 O 172.6 87.6 95.9 REMARK 620 5 HOH A 236 O 92.8 93.1 82.9 93.4 REMARK 620 6 HOH A 237 O 94.2 91.5 92.9 79.9 171.7 REMARK 620 N 1 2 3 4 5 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 IRI A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 110 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 111 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 112 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IRI A 114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SPM A 115 DBREF 4P5J A -1 84 GB 62226 V01418.1 610 695 SEQADV 4P5J U A 26 GB 62226 C 637 CONFLICT SEQADV 4P5J G A 28 GB 62226 C 639 CONFLICT SEQRES 1 A 86 U U A G C U C G C C A G U SEQRES 2 A 86 U A G C G A G G U C U G U SEQRES 3 A 86 C U C G A C A C G A C A G SEQRES 4 A 86 A U A A U C G G G U G C A SEQRES 5 A 86 A C U C C C G C C C C U C SEQRES 6 A 86 U U C C G A G G G U C A U SEQRES 7 A 86 C G G A A C C A23 MODRES 4P5J A23 A 84 A MODIFIED RESIDUE HET A23 A 84 25 HET MG A 101 1 HET MG A 102 1 HET IRI A 103 7 HET IRI A 104 7 HET IRI A 105 7 HET IRI A 106 7 HET IRI A 107 7 HET IRI A 108 7 HET IRI A 109 7 HET IRI A 110 7 HET IRI A 111 7 HET IRI A 112 7 HET IRI A 113 7 HET IRI A 114 7 HET SPM A 115 14 HETNAM A23 ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM IRI IRIDIUM HEXAMMINE ION HETNAM SPM SPERMINE FORMUL 1 A23 C10 H13 N5 O9 P2 FORMUL 2 MG 2(MG 2+) FORMUL 4 IRI 12(H18 IR N6 3+) FORMUL 16 SPM C10 H26 N4 FORMUL 17 HOH *126(H2 O) LINK O3' C A 83 P A23 A 84 1555 1555 1.59 LINK OP2 A A 40 MG MG A 102 1555 1555 2.01 LINK MG MG A 101 O HOH A 224 1555 1555 2.03 LINK MG MG A 101 O HOH A 226 1555 1555 2.13 LINK MG MG A 101 O HOH A 227 1555 1555 2.02 LINK MG MG A 101 O HOH A 229 1555 1555 2.33 LINK MG MG A 101 O HOH A 236 1555 1555 2.10 LINK MG MG A 101 O HOH A 237 1555 1555 2.20 LINK MG MG A 102 O HOH A 225 1555 1555 2.25 LINK MG MG A 102 O HOH A 228 1555 1555 2.38 LINK MG MG A 102 O HOH A 244 1555 1555 2.12 LINK MG MG A 102 O HOH A 252 1555 1555 2.24 LINK MG MG A 102 O HOH A 273 1555 1555 2.14 SITE 1 AC1 6 HOH A 224 HOH A 226 HOH A 227 HOH A 229 SITE 2 AC1 6 HOH A 236 HOH A 237 SITE 1 AC2 6 A A 40 HOH A 225 HOH A 228 HOH A 244 SITE 2 AC2 6 HOH A 252 HOH A 273 SITE 1 AC3 11 G A 44 G A 45 G A 46 A A 51 SITE 2 AC3 11 HOH A 258 HOH A 272 HOH A 275 HOH A 284 SITE 3 AC3 11 HOH A 286 HOH A 287 HOH A 325 SITE 1 AC4 4 U A 26 C A 30 HOH A 311 HOH A 319 SITE 1 AC5 10 C A 56 G A 57 C A 58 G A 71 SITE 2 AC5 10 G A 72 HOH A 248 HOH A 249 HOH A 290 SITE 3 AC5 10 HOH A 291 HOH A 310 SITE 1 AC6 6 C A 5 G A 6 G A 78 G A 79 SITE 2 AC6 6 A23 A 84 HOH A 309 SITE 1 AC7 3 G A 45 C A 60 U A 62 SITE 1 AC8 5 U A 47 G A 48 A A 50 HOH A 203 SITE 2 AC8 5 HOH A 268 SITE 1 AC9 6 A A 17 G A 18 G A 19 U A 39 SITE 2 AC9 6 HOH A 282 HOH A 303 SITE 1 AD1 3 C A 60 C A 61 A A 75 SITE 1 AD2 6 C A 43 G A 44 G A 57 C A 58 SITE 2 AD2 6 C A 59 U A 73 SITE 1 AD3 3 A A 1 G A 2 U A 22 SITE 1 AD4 4 U A 11 U A 12 G A 28 C A 83 SITE 1 AD5 5 G A 14 U A 39 A A 40 A A 41 SITE 2 AD5 5 HOH A 273 SITE 1 AD6 4 G A 68 G A 78 G A 79 A A 80 CRYST1 55.270 101.570 111.610 90.00 90.00 90.00 I 2 2 2 8 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 0.018093 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008960 0.00000