HEADER DEOXYRIBONUCLEIC ACID 18-SEP-89 ZDB020 TITLE CRYSTAL AND MOLECULAR STRUCTURE OF THE AMMONIUM SALT OF THE TITLE 2 DINUCLEOSIDE MONOPHOSPHATE D(CPG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS Z-DNA, DOUBLE HELIX EXPDTA X-RAY DIFFRACTION AUTHOR B.RAMAKRISHNAN,M.A.VISWAMITRA REVDAT 2 21-SEP-01 5 REVDAT 1 18-SEP-89 0 JRNL AUTH B.RAMAKRISHNAN,M.A.VISWAMITRA JRNL TITL CRYSTAL AND MOLECULAR STRUCTURE OF THE AMMONIUM JRNL TITL 2 SALT OF THE DINUCLEOSIDE MONOPHOSPHATE D(CPG) JRNL REF J.BIOMOL.STRUCT.DYN. V. 6 511 1988 JRNL REFN ASTM JBSDD6 US ISSN 0739-1102 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 0.85 ANGSTROM. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 1.50 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 : 2778 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) : 0.136 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 : 76 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 13 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 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 106 REMARK 106 ALL HYDROGEN BONDS BETWEEN BASE PAIRS NOT MENTIONED IN REMARK 106 REMARKS 102 AND 103 FOLLOW THE CONVENTIONAL WATSON-CRICK REMARK 106 HYDROGEN BONDING PATTERN. THEY HAVE NOT BEEN PRESENTED ON REMARK 106 *CONECT* RECORDS IN THIS ENTRY. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 291.0 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS CAD4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2778 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.850 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: ACETONE, NH4CL 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+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 6.44000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.82100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 8.72200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 13.82100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 6.44000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 8.72200 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 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, 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 SEQRES 1 A 2 C G SEQRES 1 B 2 C G HET NH4 5 1 HET NH4 6 1 HETNAM NH4 AMMONIUM ION FORMUL 3 NH4 2(H4 N1 1+) FORMUL 5 HOH *13(H2 O1) CRYST1 12.880 17.444 27.642 90.00 90.00 90.00 P 21 21 21 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 0.077640 0.000000 0.000000 0.00000 SCALE2 0.000000 0.057326 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036177 0.00000 ATOM 1 O5* C A 1 6.066 26.829 24.737 1.00 3.90 O ATOM 2 C5* C A 1 7.200 27.195 24.131 1.00 2.80 C ATOM 3 C4* C A 1 7.986 26.096 23.374 1.00 1.80 C ATOM 4 O4* C A 1 8.514 25.207 24.297 1.00 3.20 O ATOM 5 C3* C A 1 7.174 25.224 22.418 1.00 0.70 C ATOM 6 O3* C A 1 7.960 24.781 21.320 1.00 2.20 O ATOM 7 C2* C A 1 6.826 24.108 23.330 1.00 3.00 C ATOM 8 C1* C A 1 8.037 23.933 24.104 1.00 2.80 C ATOM 9 N1 C A 1 7.831 23.270 25.439 1.00 2.20 N ATOM 10 C2 C A 1 7.651 21.892 25.536 1.00 1.10 C ATOM 11 O2 C A 1 7.599 21.317 24.510 1.00 2.20 O ATOM 12 N3 C A 1 7.599 21.282 26.722 1.00 2.10 N ATOM 13 C4 C A 1 7.664 21.979 27.863 1.00 2.40 C ATOM 14 N4 C A 1 7.651 21.351 29.010 1.00 2.30 N ATOM 15 C5 C A 1 7.715 23.445 27.780 1.00 2.50 C ATOM 16 C6 C A 1 7.895 24.020 26.592 1.00 2.40 C ATOM 17 P G A 2 8.053 25.637 19.971 1.00 2.40 P ATOM 18 O1P G A 2 6.736 26.375 19.723 1.00 2.80 O ATOM 19 O2P G A 2 8.591 24.718 18.946 1.00 3.90 O ATOM 20 O5* G A 2 9.068 26.759 20.331 1.00 3.00 O ATOM 21 C5* G A 2 10.446 26.410 20.649 1.00 2.70 C ATOM 22 C4* G A 2 11.206 27.509 21.091 1.00 1.80 C ATOM 23 O4* G A 2 10.562 28.163 22.235 1.00 1.60 O ATOM 24 C3* G A 2 12.610 27.265 21.478 1.00 2.70 C ATOM 25 O3* G A 2 13.563 27.265 20.461 1.00 4.40 O ATOM 26 C2* G A 2 12.919 28.329 22.578 1.00 1.20 C ATOM 27 C1* G A 2 11.540 28.556 23.142 1.00 1.90 C ATOM 28 N9 G A 2 11.270 28.172 24.460 1.00 1.70 N ATOM 29 C8 G A 2 10.742 28.835 25.519 1.00 1.50 C ATOM 30 N7 G A 2 10.497 28.155 26.605 1.00 2.00 N ATOM 31 C5 G A 2 10.819 26.881 26.196 1.00 1.80 C ATOM 32 C6 G A 2 10.755 25.678 26.943 1.00 2.20 C ATOM 33 O6 G A 2 10.459 25.486 28.079 1.00 2.90 O ATOM 34 N1 G A 2 11.103 24.579 26.097 1.00 2.00 N ATOM 35 C2 G A 2 11.425 24.718 24.856 1.00 1.40 C ATOM 36 N2 G A 2 11.759 23.480 24.170 1.00 2.20 N ATOM 37 N3 G A 2 11.605 25.782 24.173 1.00 2.20 N ATOM 38 C4 G A 2 11.231 26.846 24.883 1.00 1.60 C TER 39 G A 2 ATOM 40 O5* C B 3 12.558 15.996 27.899 1.00 4.30 O ATOM 41 C5* C B 3 11.450 15.316 27.421 1.00 4.00 C ATOM 42 C4* C B 3 10.806 16.083 26.268 1.00 1.90 C ATOM 43 O4* C B 3 10.214 17.339 26.774 1.00 3.50 O ATOM 44 C3* C B 3 11.824 16.537 25.174 1.00 1.30 C ATOM 45 O3* C B 3 11.103 16.624 23.869 1.00 3.10 O ATOM 46 C2* C B 3 12.094 17.985 25.624 1.00 2.80 C ATOM 47 C1* C B 3 10.703 18.403 26.039 1.00 4.30 C ATOM 48 N1 C B 3 10.806 19.607 27.020 1.00 1.10 N ATOM 49 C2 C B 3 10.781 20.863 26.459 1.00 0.90 C ATOM 50 O2 C B 3 10.845 20.968 25.254 1.00 3.00 O ATOM 51 N3 C B 3 10.871 21.945 27.316 1.00 1.40 N ATOM 52 C4 C B 3 10.781 21.770 28.632 1.00 2.00 C ATOM 53 N4 C B 3 10.755 22.869 29.395 1.00 2.90 N ATOM 54 C5 C B 3 10.819 20.427 29.187 1.00 2.10 C ATOM 55 C6 C B 3 10.806 19.415 28.311 1.00 1.00 C ATOM 56 P G B 4 11.253 15.506 22.769 1.00 1.50 P ATOM 57 O1P G B 4 12.571 14.880 22.813 1.00 2.90 O ATOM 58 O2P G B 4 10.819 16.223 21.481 1.00 2.40 O ATOM 59 O5* G B 4 10.240 14.409 23.111 1.00 2.40 O ATOM 60 C5* G B 4 8.771 14.705 23.098 1.00 2.20 C ATOM 61 C4* G B 4 7.960 13.676 23.648 1.00 1.90 C ATOM 62 O4* G B 4 8.320 13.467 25.024 1.00 2.70 O ATOM 63 C3* G B 4 6.517 13.833 23.551 1.00 2.90 C ATOM 64 O3* G B 4 5.925 13.100 22.525 1.00 5.90 O ATOM 65 C2* G B 4 6.015 13.432 24.988 1.00 2.10 C ATOM 66 C1* G B 4 7.226 13.414 25.793 1.00 1.80 C ATOM 67 N9 G B 4 7.277 14.444 26.868 1.00 1.20 N ATOM 68 C8 G B 4 7.638 14.287 28.087 1.00 2.10 C ATOM 69 N7 G B 4 7.741 15.386 28.748 1.00 4.50 N ATOM 70 C5 G B 4 7.470 16.345 27.869 1.00 1.50 C ATOM 71 C6 G B 4 7.483 17.793 27.907 1.00 2.20 C ATOM 72 O6 G B 4 7.818 18.496 28.952 1.00 2.00 O ATOM 73 N1 G B 4 7.264 18.351 26.733 1.00 1.90 N ATOM 74 C2 G B 4 6.955 17.723 25.613 1.00 0.90 C ATOM 75 N2 G B 4 6.685 18.491 24.549 1.00 3.20 N ATOM 76 N3 G B 4 6.852 16.380 25.494 1.00 1.80 N ATOM 77 C4 G B 4 7.200 15.769 26.683 1.00 1.10 C TER 78 G B 4 HETATM 79 N NH4 5 2.331 8.146 6.388 1.00 2.20 N HETATM 80 N NH4 6 4.109 2.843 10.084 1.00 2.30 N HETATM 81 O HOH 7 8.514 28.538 28.549 1.00 3.80 O HETATM 82 O HOH 8 2.447 7.710 9.111 1.00 6.10 O HETATM 83 O HOH 9 12.172 20.584 22.619 1.00 4.80 O HETATM 84 O HOH 10 9.428 14.304 30.871 1.00 4.40 O HETATM 85 O HOH 11 10.433 22.241 32.313 1.00 6.40 O HETATM 86 O HOH 12 9.286 20.462 22.556 1.00 6.80 O HETATM 87 O HOH 13 6.182 20.532 21.423 1.00 7.90 O HETATM 88 O HOH 14 12.056 22.939 21.174 1.00 10.00 O HETATM 89 O HOH 15 9.338 25.974 30.636 1.00 6.00 O HETATM 90 O HOH 16 8.308 18.055 31.401 1.00 8.20 O HETATM 91 O HOH 17 8.179 23.462 31.426 1.00 6.60 O HETATM 92 O HOH 18 2.937 3.838 7.049 1.00 9.10 O HETATM 93 O HOH 19 9.055 20.095 33.087 1.00 16.00 O MASTER 204 0 2 0 0 0 0 6 91 2 0 2 END