HEADER DEOXYRIBONUCLEIC ACID 04-MAY-94 UDBS38 TITLE CRYSTAL STRUCTURE OF A PARALLEL-STRANDED DUPLEX OF A TITLE 2 DEOXYCYTIDYLYL-(3'-5')-DEOXYCYTIDINE ANALOGUE CONTAINING TITLE 3 INTRANUCLEOSIDYL C(3')-C(5') ETHYLENE BRIDGES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-(C2H2)D(*CP*C)-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, MODIFIED EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,P.LUBINI,M.BOLLI,M.DOBLER,C.LEUMANN REVDAT 2 21-SEP-01 5 REVDAT 1 04-MAY-94 0 JRNL AUTH M.EGLI,P.LUBINI,M.BOLLI,M.DOBLER,C.LEUMANN JRNL TITL CRYSTAL STRUCTURE OF A PARALLEL-STRANDED DUPLEX OF JRNL TITL 2 A DEOXYCYTIDYLYL-(3'-5')-DEOXYCYTIDINE ANALOGUE JRNL TITL 3 CONTAINING INTRANUCLEOSIDYL C(3')-C(5') ETHYLENE JRNL TITL 4 BRIDGES JRNL REF J.AM.CHEM.SOC. V. 115 5855 1993 JRNL REFN ASTM JACSAT US ISSN 0002-7863 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-92 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.093 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.093 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 2556 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 70 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 NULL COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY THE NUCLEIC ACID DATABASE REMARK 100 ON 13-OCT-1995. REMARK 100 THE NDB ID CODE IS UDBS38. REMARK 102 REMARK 102 BASES +C A 1 AND +C B 3 ARE MISPAIRED. REMARK 102 BASES +C A 2 AND +C B 4 ARE MISPAIRED. REMARK 103 REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE REMARK 103 FOLLOWING ATOMS: REMARK 103 O2 +C A 1 AND N4 +C B 3 REMARK 103 N4 +C A 1 AND O2 +C B 3 REMARK 103 N4 +C A 2 AND O2 +C B 4 REMARK 103 O2 +C A 2 AND N4 +C B 4 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) : 273.0 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) : 0.7100 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 : 2556 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL 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: NH4+ 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 9.55350 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 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 +C SEQRES 1 B 2 +C +C MODRES +C A 1 C CYTOSINE MODIFIED WITH C2H2 MODRES +C A 2 C CYTOSINE MODIFIED WITH C2H2 MODRES +C B 3 C CYTOSINE MODIFIED WITH C2H2 MODRES +C B 4 C CYTOSINE MODIFIED WITH C2H2 HET ETD A 1 2 HET ETD A 2 2 HET ETD B 3 2 HET ETD B 4 2 HET MOH 12 2 HET MOH 13 2 HET MOH 14 2 HET MOH 15 2 HETNAM ETD ETHENYLENE GROUP HETNAM MOH METHANOL FORMUL 3 ETD 4(C2 H2) FORMUL 7 HOH *7(H2 O1) FORMUL 8 MOH 4(C1 H4 O1) LINK C10 ETD A 1 C5* +C A 1 LINK C11 ETD A 1 C3* +C A 1 LINK C10 ETD A 2 C5* +C A 2 LINK C11 ETD A 2 C3* +C A 2 LINK C10 ETD B 3 C5* +C B 3 LINK C11 ETD B 3 C3* +C B 3 LINK C10 ETD B 4 C5* +C B 4 LINK C11 ETD B 4 C3* +C B 4 LINK C10 ETD A 2 C3* +C A 2 LINK C11 ETD A 2 C5* +C A 2 CRYST1 13.370 19.107 13.370 90.00 91.45 90.00 P 1 21 1 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 0.074794 0.000000 0.001893 0.00000 SCALE2 0.000000 0.052337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.074818 0.00000 ATOM 1 O5* +C A 1 1.829 -3.583 8.626 1.00 10.00 O ATOM 2 C5* +C A 1 2.898 -4.140 8.019 1.00 10.00 C ATOM 3 C4* +C A 1 3.140 -3.634 6.680 1.00 10.00 C ATOM 4 O4* +C A 1 2.884 -2.237 6.560 1.00 10.00 O ATOM 5 C3* +C A 1 4.708 -3.816 6.337 1.00 10.00 C ATOM 6 O3* +C A 1 4.733 -4.834 5.306 1.00 10.00 O ATOM 7 C2* +C A 1 5.130 -2.448 5.876 1.00 10.00 C ATOM 8 C1* +C A 1 3.831 -1.727 5.620 1.00 10.00 C ATOM 9 N1 +C A 1 3.831 -0.291 5.725 1.00 10.00 N ATOM 10 C2 +C A 1 3.267 0.485 4.727 1.00 10.00 C ATOM 11 O2 +C A 1 2.704 -0.009 3.782 1.00 10.00 O ATOM 12 N3 +C A 1 3.386 1.838 4.866 1.00 10.00 N ATOM 13 C4 +C A 1 4.020 2.436 5.885 1.00 10.00 C ATOM 14 N4 +C A 1 4.147 3.734 5.881 1.00 10.00 N ATOM 15 C5 +C A 1 4.572 1.626 6.925 1.00 10.00 C ATOM 16 C6 +C A 1 4.427 0.279 6.839 1.00 10.00 C ATOM 17 P +C A 2 6.117 -5.337 4.655 1.00 10.00 P ATOM 18 O1P +C A 2 5.972 -6.768 4.457 1.00 10.00 O ATOM 19 O2P +C A 2 7.268 -4.795 5.394 1.00 10.00 O ATOM 20 O5* +C A 2 6.163 -4.617 3.230 1.00 10.00 O ATOM 21 C5* +C A 2 5.376 -5.079 2.167 1.00 10.00 C ATOM 22 C4* +C A 2 4.058 -4.305 1.910 1.00 10.00 C ATOM 23 O4* +C A 2 4.106 -3.050 2.499 1.00 10.00 O ATOM 24 C3* +C A 2 3.955 -4.108 0.373 1.00 10.00 C ATOM 25 O3* +C A 2 2.671 -4.399 -0.133 1.00 10.00 O ATOM 26 C2* +C A 2 4.254 -2.664 0.167 1.00 10.00 C ATOM 27 C1* +C A 2 4.112 -2.075 1.434 1.00 10.00 C ATOM 28 N1 +C A 2 4.910 -0.954 1.930 1.00 10.00 N ATOM 29 C2 +C A 2 4.574 0.369 1.616 1.00 10.00 C ATOM 30 O2 +C A 2 3.632 0.562 0.818 1.00 10.00 O ATOM 31 N3 +C A 2 5.279 1.378 2.104 1.00 10.00 N ATOM 32 C4 +C A 2 6.338 1.145 2.916 1.00 10.00 C ATOM 33 N4 +C A 2 6.981 2.134 3.447 1.00 10.00 N ATOM 34 C5 +C A 2 6.701 -0.178 3.222 1.00 10.00 C ATOM 35 C6 +C A 2 5.929 -1.150 2.767 1.00 10.00 C TER 36 +C A 2 HETATM 37 C10 ETD A 1 4.177 -3.753 8.692 1.00 10.00 C HETATM 38 C11 ETD A 1 5.246 -4.364 7.668 1.00 10.00 C HETATM 39 C10 ETD A 2 5.054 -5.040 -0.207 1.00 10.00 C HETATM 40 C11 ETD A 2 6.212 -4.966 0.845 1.00 10.00 C ATOM 41 O5* +C B 3 -2.136 8.835 4.623 1.00 10.00 O ATOM 42 C5* +C B 3 -1.458 9.359 3.519 1.00 10.00 C ATOM 43 C4* +C B 3 -0.076 8.904 3.415 1.00 10.00 C ATOM 44 O4* +C B 3 0.067 7.508 3.605 1.00 10.00 O ATOM 45 C3* +C B 3 0.298 9.133 1.897 1.00 10.00 C ATOM 46 O3* +C B 3 1.319 10.102 1.814 1.00 10.00 O ATOM 47 C2* +C B 3 0.758 7.771 1.421 1.00 10.00 C ATOM 48 C1* +C B 3 1.020 7.010 2.751 1.00 10.00 C ATOM 49 N1 +C B 3 0.888 5.563 2.676 1.00 10.00 N ATOM 50 C2 +C B 3 1.883 4.828 3.308 1.00 10.00 C ATOM 51 O2 +C B 3 2.782 5.312 3.922 1.00 10.00 O ATOM 52 N3 +C B 3 1.762 3.435 3.193 1.00 10.00 N ATOM 53 C4 +C B 3 0.722 2.860 2.467 1.00 10.00 C ATOM 54 N4 +C B 3 0.750 1.536 2.384 1.00 10.00 N ATOM 55 C5 +C B 3 -0.248 3.716 1.946 1.00 10.00 C ATOM 56 C6 +C B 3 -0.180 5.012 2.092 1.00 10.00 C ATOM 57 P +C B 4 2.017 10.628 0.457 1.00 10.00 P ATOM 58 O1P +C B 4 2.164 12.091 0.624 1.00 10.00 O ATOM 59 O2P +C B 4 1.278 10.096 -0.721 1.00 10.00 O ATOM 60 O5* +C B 4 3.472 9.871 0.400 1.00 10.00 O ATOM 61 C5* +C B 4 4.532 10.417 1.280 1.00 10.00 C ATOM 62 C4* +C B 4 4.732 9.620 2.566 1.00 10.00 C ATOM 63 O4* +C B 4 4.164 8.284 2.508 1.00 10.00 O ATOM 64 C3* +C B 4 6.196 9.414 2.732 1.00 10.00 C ATOM 65 O3* +C B 4 6.692 9.712 4.003 1.00 10.00 O ATOM 66 C2* +C B 4 6.440 7.895 2.478 1.00 10.00 C ATOM 67 C1* +C B 4 5.210 7.327 2.581 1.00 10.00 C ATOM 68 N1 +C B 4 4.723 6.207 1.767 1.00 10.00 N ATOM 69 C2 +C B 4 5.039 4.954 2.117 1.00 10.00 C ATOM 70 O2 +C B 4 5.817 4.743 3.062 1.00 10.00 O ATOM 71 N3 +C B 4 4.546 3.915 1.377 1.00 10.00 N ATOM 72 C4 +C B 4 3.733 4.167 0.305 1.00 10.00 C ATOM 73 N4 +C B 4 3.263 3.109 -0.361 1.00 10.00 N ATOM 74 C5 +C B 4 3.406 5.463 -0.087 1.00 10.00 C ATOM 75 C6 +C B 4 3.860 6.472 0.682 1.00 10.00 C TER 76 +C B 4 HETATM 77 C10 ETD B 3 -2.112 9.101 2.291 1.00 10.00 C HETATM 78 C11 ETD B 3 -1.020 9.596 1.248 1.00 10.00 C HETATM 79 C10 ETD B 4 5.811 10.293 0.476 1.00 10.00 C HETATM 80 C11 ETD B 4 6.838 10.322 1.677 1.00 10.00 C HETATM 81 C MOH 12 0.410 5.736 6.611 1.00 10.00 C HETATM 82 O MOH 12 -0.067 4.668 5.852 1.00 10.00 O HETATM 83 C MOH 13 2.452 3.701 9.454 1.00 10.00 C HETATM 84 O MOH 13 1.665 3.571 10.590 1.00 10.00 O HETATM 85 C MOH 14 10.343 1.487 3.744 1.00 10.00 C HETATM 86 O MOH 14 9.394 1.699 4.764 1.00 10.00 O HETATM 87 C MOH 15 -0.015 -0.189 5.680 1.00 10.00 C HETATM 88 O MOH 15 0.517 0.720 6.609 1.00 10.00 O HETATM 89 O HOH 5 -2.089 17.334 2.184 1.00 10.00 O HETATM 90 O HOH 6 8.577 -2.554 4.674 1.00 10.00 O HETATM 91 O HOH 7 0.768 13.105 2.919 1.00 10.00 O HETATM 92 O HOH 8 3.558 -7.730 5.872 1.00 10.00 O HETATM 93 O HOH 9 12.367 2.593 7.505 1.00 10.00 O HETATM 94 O HOH 10 8.815 -1.731 6.733 1.00 10.00 O HETATM 95 O HOH 11 -0.363 15.703 2.894 1.00 10.00 O CONECT 2 37 CONECT 5 38 CONECT 21 39 40 CONECT 24 39 40 CONECT 37 2 38 CONECT 38 5 37 CONECT 39 21 24 40 CONECT 40 21 24 39 CONECT 42 77 CONECT 45 78 CONECT 61 79 CONECT 64 80 CONECT 77 42 78 CONECT 78 45 77 CONECT 79 61 80 CONECT 80 64 79 CONECT 81 82 CONECT 82 81 CONECT 83 84 CONECT 84 83 CONECT 85 86 CONECT 86 85 CONECT 87 88 CONECT 88 87 MASTER 181 0 8 0 0 0 0 6 93 2 24 2 END