HEADER DEOXYRIBONUCLEIC ACID 18-AUG-88 UDB005 TITLE CRYSTAL AND MOLECULAR STRUCTURE OF THE SODIUM SALT OF THE TITLE 2 DINUCLEOTIDE DUPLEX 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 U-DNA, DOUBLE HELIX, PARALLEL HELIX EXPDTA X-RAY DIFFRACTION AUTHOR M.COLL,X.SOLANS,M.FONT-ALTABA,J.A.SUBIRANA REVDAT 2 21-SEP-01 5 REVDAT 1 18-AUG-88 0 JRNL AUTH M.COLL,X.SOLANS,M.FONT-ALTABA,J.A.SUBIRANA JRNL TITL CRYSTAL AND MOLECULAR STRUCTURE OF THE SODIUM SALT JRNL TITL 2 OF THE DINUCLEOTIDE DUPLEX D(CPG) JRNL REF J.BIOMOL.STRUCT.DYN. V. 4 797 1987 JRNL REFN ASTM JBSDD6 US ISSN 0739-1102 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 0.86 ANGSTROM. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.86 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 : 2356 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) : 0.041 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 : 1 REMARK 3 SOLVENT ATOMS : 7 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) : NULL REMARK 200 PH : 5.30 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) : 0.7100 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : PHILLIPS PW-1100 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2356 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.860 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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: GAMMA-BUTYROLACTONE 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 5.32000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.30900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 5.59200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.30900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 5.32000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 5.59200 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 NA 5 1 HETNAM NA SODIUM ION FORMUL 3 NA NA1 1+ FORMUL 4 HOH *7(H2 O1) CRYST1 10.640 11.184 44.618 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 0.093985 0.000000 0.000000 0.00000 SCALE2 0.000000 0.089413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022412 0.00000 ATOM 1 O5* C A 1 2.508 7.115 29.020 1.00 6.28 O ATOM 2 C5* C A 1 2.822 6.369 30.197 1.00 5.06 C ATOM 3 C4* C A 1 3.692 7.151 31.126 1.00 3.44 C ATOM 4 O4* C A 1 4.997 7.355 30.514 1.00 4.05 O ATOM 5 C3* C A 1 3.147 8.528 31.447 1.00 3.03 C ATOM 6 O3* C A 1 3.343 8.747 32.892 1.00 3.68 O ATOM 7 C2* C A 1 3.961 9.478 30.644 1.00 3.21 C ATOM 8 C1* C A 1 5.298 8.734 30.456 1.00 3.49 C ATOM 9 N1 C A 1 5.901 9.012 29.185 1.00 3.34 N ATOM 10 C2 C A 1 7.010 9.835 29.118 1.00 4.26 C ATOM 11 O2 C A 1 7.586 10.179 30.153 1.00 6.00 O ATOM 12 N3 C A 1 7.410 10.318 27.940 1.00 4.21 N ATOM 13 C4 C A 1 6.765 10.037 26.811 1.00 4.15 C ATOM 14 N4 C A 1 7.179 10.529 25.682 1.00 5.54 N ATOM 15 C5 C A 1 5.653 9.147 26.905 1.00 5.27 C ATOM 16 C6 C A 1 5.248 8.679 28.060 1.00 3.76 C ATOM 17 P G A 2 2.370 9.756 33.660 1.00 4.00 P ATOM 18 O1P G A 2 2.693 9.570 35.083 1.00 5.38 O ATOM 19 O2P G A 2 0.970 9.557 33.209 1.00 6.49 O ATOM 20 O5* G A 2 2.788 11.211 33.178 1.00 3.86 O ATOM 21 C5* G A 2 4.040 11.796 33.562 1.00 4.05 C ATOM 22 C4* G A 2 4.149 13.154 32.955 1.00 2.89 C ATOM 23 O4* G A 2 4.141 13.072 31.523 1.00 3.91 O ATOM 24 C3* G A 2 3.007 14.096 33.276 1.00 3.77 C ATOM 25 O3* G A 2 3.511 15.429 33.330 1.00 4.89 O ATOM 26 C2* G A 2 2.008 13.915 32.152 1.00 3.50 C ATOM 27 C1* G A 2 2.956 13.623 31.010 1.00 3.04 C ATOM 28 N9 G A 2 2.431 12.720 30.006 1.00 2.68 N ATOM 29 C8 G A 2 1.500 11.704 30.135 1.00 3.59 C ATOM 30 N7 G A 2 1.345 11.005 29.064 1.00 3.52 N ATOM 31 C5 G A 2 2.249 11.547 28.154 1.00 2.63 C ATOM 32 C6 G A 2 2.541 11.226 26.824 1.00 2.99 C ATOM 33 O6 G A 2 2.095 10.355 26.146 1.00 4.48 O ATOM 34 N1 G A 2 3.558 12.033 26.320 1.00 2.90 N ATOM 35 C2 G A 2 4.161 13.061 26.963 1.00 3.38 C ATOM 36 N2 G A 2 5.095 13.725 26.267 1.00 4.46 N ATOM 37 N3 G A 2 3.886 13.407 28.190 1.00 3.05 N ATOM 38 C4 G A 2 2.904 12.626 28.721 1.00 2.46 C TER 39 G A 2 ATOM 40 O5* C B 3 12.287 17.455 26.632 1.00 7.02 O ATOM 41 C5* C B 3 13.256 16.834 25.758 1.00 4.43 C ATOM 42 C4* C B 3 12.581 15.786 24.901 1.00 3.06 C ATOM 43 O4* C B 3 12.262 14.652 25.691 1.00 5.07 O ATOM 44 C3* C B 3 11.244 16.269 24.312 1.00 3.01 C ATOM 45 O3* C B 3 11.143 15.757 22.978 1.00 2.93 O ATOM 46 C2* C B 3 10.209 15.631 25.214 1.00 3.71 C ATOM 47 C1* C B 3 10.882 14.343 25.620 1.00 3.89 C ATOM 48 N1 C B 3 10.445 13.886 26.896 1.00 3.76 N ATOM 49 C2 C B 3 9.731 12.679 26.958 1.00 4.59 C ATOM 50 O2 C B 3 9.645 11.950 26.003 1.00 6.49 O ATOM 51 N3 C B 3 9.197 12.391 28.158 1.00 4.32 N ATOM 52 C4 C B 3 9.254 13.161 29.260 1.00 4.58 C ATOM 53 N4 C B 3 8.679 12.778 30.363 1.00 5.19 N ATOM 54 C5 C B 3 10.021 14.349 29.171 1.00 4.20 C ATOM 55 C6 C B 3 10.576 14.696 28.002 1.00 3.91 C ATOM 56 P G B 4 10.277 16.533 21.907 1.00 3.04 P ATOM 57 O1P G B 4 10.453 15.854 20.658 1.00 4.61 O ATOM 58 O2P G B 4 10.602 17.988 21.952 1.00 3.99 O ATOM 59 O5* G B 4 8.749 16.420 22.416 1.00 3.23 O ATOM 60 C5* G B 4 8.056 15.187 22.233 1.00 3.12 C ATOM 61 C4* G B 4 6.702 15.273 22.885 1.00 2.90 C ATOM 62 O4* G B 4 6.872 15.469 24.317 1.00 3.24 O ATOM 63 C3* G B 4 5.851 16.411 22.407 1.00 3.64 C ATOM 64 O3* G B 4 4.450 15.963 22.447 1.00 4.55 O ATOM 65 C2* G B 4 6.066 17.528 23.424 1.00 3.30 C ATOM 66 C1* G B 4 6.263 16.673 24.683 1.00 3.01 C ATOM 67 N9 G B 4 7.083 17.321 25.704 1.00 2.83 N ATOM 68 C8 G B 4 8.095 18.260 25.495 1.00 3.74 C ATOM 69 N7 G B 4 8.724 18.541 26.615 1.00 3.83 N ATOM 70 C5 G B 4 8.122 17.746 27.574 1.00 2.89 C ATOM 71 C6 G B 4 8.365 17.592 28.966 1.00 3.48 C ATOM 72 O6 G B 4 9.225 18.180 29.640 1.00 6.07 O ATOM 73 N1 G B 4 7.561 16.627 29.533 1.00 3.58 N ATOM 74 C2 G B 4 6.593 15.923 28.890 1.00 3.24 C ATOM 75 N2 G B 4 5.929 15.031 29.617 1.00 4.46 N ATOM 76 N3 G B 4 6.323 16.069 27.610 1.00 3.11 N ATOM 77 C4 G B 4 7.131 16.978 27.025 1.00 2.76 C TER 78 G B 4 HETATM 79 NA NA 5 0.326 8.618 26.396 1.00 7.45 NA HETATM 80 O HOH 6 8.738 19.277 20.404 1.00 5.52 O HETATM 81 O HOH 7 10.398 8.777 24.022 1.00 8.16 O HETATM 82 O HOH 8 -0.388 14.181 38.157 1.00 4.49 O HETATM 83 O HOH 9 8.072 9.659 22.590 1.00 5.57 O HETATM 84 O HOH 10 0.045 7.295 32.080 1.00 12.56 O HETATM 85 O HOH 11 0.487 14.994 35.672 1.00 8.08 O HETATM 86 O HOH 12 1.231 16.981 33.812 1.00 9.23 O MASTER 204 0 1 0 0 0 0 6 84 2 0 2 END