HEADER RIBONUCLEIC ACID 18-AUG-88 DRB003 TITLE NUCLEIC ACID-MUTAGEN INTERACTIONS: CRYSTAL STRUCTURE OF TITLE 2 ADENYLYL-3',5'-URIDINE PLUS 9-AMINOACRIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*AP*U)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS U-RNA, SINGLE STRAND, COMPLEXED WITH DRUG, OPEN EXPDTA X-RAY DIFFRACTION AUTHOR N.C.SEEMAN,R.O.DAY,A.RICH REVDAT 2 21-SEP-01 5 REVDAT 1 18-AUG-88 0 JRNL AUTH N.C.SEEMAN,R.O.DAY,A.RICH JRNL TITL NUCLEIC ACID-MUTAGEN INTERACTIONS: CRYSTAL JRNL TITL 2 STRUCTURE OF ADENYLYL-3',5'-URIDINE PLUS JRNL TITL 3 9-AMINOACRIDINE JRNL REF NATURE V. 253 324 1975 JRNL REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROM. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 2874 REMARK 3 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.070 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 56 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 9 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 NULL COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 103 REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE REMARK 103 FOLLOWING ATOMS: REMARK 103 N7 A A 1 AND N3 U A 2 REMARK 103 N6 A A 1 AND O4 U A 2 REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : SYNTEX P1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2874 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ISOPROPANOL, NA CACODYLATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,1/2+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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 13.33850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 0 HOH 7 DISTANCE = 5.03 ANGSTROMS SEQRES 1 A 2 A U HET AA 3 15 HETNAM AA 9-AMINOACRIDINE FORMUL 2 AA C13 H11 N2 1+ FORMUL 3 HOH *9(H2 O1) CRYST1 13.261 26.677 6.922 90.00 95.08 90.00 P 1 21 1 2 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 0.075409 0.000000 0.006704 0.00000 SCALE2 0.000000 0.037485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.145037 0.00000 ATOM 1 O5* A A 1 5.115 3.540 4.818 1.00 10.00 O ATOM 2 C5* A A 1 4.549 4.815 4.675 1.00 10.00 C ATOM 3 C4* A A 1 3.332 4.732 3.798 1.00 10.00 C ATOM 4 O4* A A 1 2.618 6.010 3.889 1.00 10.00 O ATOM 5 C3* A A 1 3.712 4.543 2.299 1.00 10.00 C ATOM 6 O3* A A 1 2.772 3.636 1.662 1.00 10.00 O ATOM 7 C2* A A 1 3.503 5.925 1.705 1.00 10.00 C ATOM 8 O2* A A 1 3.261 6.008 0.322 1.00 10.00 O ATOM 9 C1* A A 1 2.357 6.477 2.546 1.00 10.00 C ATOM 10 N9 A A 1 2.264 7.912 2.595 1.00 10.00 N ATOM 11 C8 A A 1 3.276 8.819 2.692 1.00 10.00 C ATOM 12 N7 A A 1 2.861 10.065 2.677 1.00 10.00 N ATOM 13 C5 A A 1 1.484 9.972 2.555 1.00 10.00 C ATOM 14 C6 A A 1 0.485 10.954 2.468 1.00 10.00 C ATOM 15 N6 A A 1 0.721 12.290 2.477 1.00 10.00 N ATOM 16 N1 A A 1 -0.803 10.535 2.339 1.00 10.00 N ATOM 17 C2 A A 1 -1.028 9.206 2.329 1.00 10.00 C ATOM 18 N3 A A 1 -0.165 8.193 2.413 1.00 10.00 N ATOM 19 C4 A A 1 1.097 8.651 2.504 1.00 10.00 C ATOM 20 H 9 A A 1 4.636 4.250 2.224 1.00 10.00 H ATOM 21 H 7 A A 1 2.749 4.002 4.114 1.00 10.00 H ATOM 22 1H 6 A A 1 4.289 5.175 5.547 1.00 10.00 H ATOM 23 2H 6 A A 1 5.152 5.442 4.285 1.00 10.00 H ATOM 24 1H2 A A 1 -1.943 8.953 2.258 1.00 10.00 H ATOM 25 1H1 A A 1 4.291 6.467 1.765 1.00 10.00 H ATOM 26 3H1 A A 1 1.523 6.130 2.241 1.00 10.00 H ATOM 27 5H1 A A 1 4.225 8.587 2.743 1.00 10.00 H ATOM 28 P U A 2 3.312 2.505 0.654 1.00 10.00 P ATOM 29 O1P U A 2 4.759 2.734 0.275 1.00 10.00 O ATOM 30 O2P U A 2 2.213 2.409 -0.366 1.00 10.00 O ATOM 31 O5* U A 2 3.319 1.187 1.534 1.00 10.00 O ATOM 32 C5* U A 2 2.164 0.365 1.670 1.00 10.00 C ATOM 33 C4* U A 2 2.276 -0.467 2.914 1.00 10.00 C ATOM 34 O4* U A 2 3.494 -1.240 2.849 1.00 10.00 O ATOM 35 C3* U A 2 2.328 0.317 4.213 1.00 10.00 C ATOM 36 O3* U A 2 1.054 0.656 4.677 1.00 10.00 O ATOM 37 C2* U A 2 3.133 -0.608 5.165 1.00 10.00 C ATOM 38 O2* U A 2 2.299 -1.555 5.836 1.00 10.00 O ATOM 39 C1* U A 2 4.074 -1.377 4.149 1.00 10.00 C ATOM 40 N1 U A 2 5.444 -0.902 4.127 1.00 10.00 N ATOM 41 C2 U A 2 6.455 -1.849 4.164 1.00 10.00 C ATOM 42 O2 U A 2 6.261 -3.047 4.211 1.00 10.00 O ATOM 43 N3 U A 2 7.734 -1.313 4.177 1.00 10.00 N ATOM 44 C4 U A 2 8.111 0.021 4.143 1.00 10.00 C ATOM 45 O4 U A 2 9.285 0.320 4.153 1.00 10.00 O ATOM 46 C5 U A 2 7.000 0.934 4.035 1.00 10.00 C ATOM 47 C6 U A 2 5.732 0.448 4.020 1.00 10.00 C ATOM 48 H 8 U A 2 2.831 1.110 4.071 1.00 10.00 H ATOM 49 H 6 U A 2 1.535 -1.051 2.881 1.00 10.00 H ATOM 50 1H 5 U A 2 2.057 -0.187 0.888 1.00 10.00 H ATOM 51 2H 5 U A 2 1.370 0.920 1.729 1.00 10.00 H ATOM 52 0H2 U A 2 5.004 1.056 3.921 1.00 10.00 H ATOM 53 0H1 U A 2 3.660 -0.123 5.798 1.00 10.00 H ATOM 54 2H1 U A 2 4.127 -2.300 4.386 1.00 10.00 H ATOM 55 6H1 U A 2 8.434 -1.905 4.165 1.00 10.00 H ATOM 56 9H1 U A 2 7.133 1.870 3.998 1.00 10.00 H TER 57 U A 2 HETATM 58 C1 AA 3 5.658 10.788 6.123 1.00 10.00 C HETATM 59 C2 AA 3 6.369 11.935 6.137 1.00 10.00 C HETATM 60 C3 AA 3 5.760 13.181 6.164 1.00 10.00 C HETATM 61 C4 AA 3 4.402 13.258 6.179 1.00 10.00 C HETATM 62 C5 AA 3 0.022 11.292 5.985 1.00 10.00 C HETATM 63 C6 AA 3 -0.756 10.167 5.908 1.00 10.00 C HETATM 64 C7 AA 3 -0.245 8.921 5.849 1.00 10.00 C HETATM 65 C8 AA 3 1.109 8.697 5.917 1.00 10.00 C HETATM 66 C9 AA 3 3.421 9.622 6.103 1.00 10.00 C HETATM 67 N10 AA 3 2.228 12.199 6.130 1.00 10.00 N HETATM 68 C11 AA 3 1.515 11.098 6.051 1.00 10.00 C HETATM 69 C12 AA 3 1.987 9.801 6.035 1.00 10.00 C HETATM 70 C13 AA 3 4.223 10.810 6.134 1.00 10.00 C HETATM 71 C14 AA 3 3.595 12.087 6.129 1.00 10.00 C HETATM 72 N9 AA 3 3.976 8.419 6.183 1.00 10.00 N HETATM 73 O HOH 4 0.356 4.855 6.284 1.00 10.00 O HETATM 74 O HOH 5 11.711 1.342 0.664 1.00 10.00 O HETATM 75 O HOH 6 7.186 3.871 0.998 1.00 10.00 O HETATM 76 O HOH 7 8.917 9.313 6.550 1.00 10.00 O HETATM 77 O HOH 8 7.210 7.299 -0.458 1.00 10.00 O HETATM 78 O HOH 9 12.742 2.905 2.812 1.00 10.00 O HETATM 79 O HOH 10 6.547 7.632 3.367 1.00 10.00 O HETATM 80 O HOH 11 10.663 2.508 4.915 1.00 10.00 O HETATM 81 O HOH 12 12.310 5.666 3.877 1.00 10.00 O CONECT 58 59 70 CONECT 59 58 60 CONECT 60 59 61 CONECT 61 60 71 CONECT 62 63 68 CONECT 63 62 64 CONECT 64 63 65 CONECT 65 64 69 CONECT 66 69 70 72 CONECT 67 68 71 CONECT 68 62 67 69 CONECT 69 65 66 68 CONECT 70 58 66 71 CONECT 71 61 67 70 CONECT 72 66 MASTER 206 0 1 0 0 0 0 6 80 1 15 1 END