HEADER DEOXYRIBONUCLEIC ACID 31-MAR-93 UDBP19 TITLE MOLECULAR STRUCTURE OF DEOXYADENYLYL-3'-METHYLPHOSPHONATE- TITLE 2 5'-THYMIDINE DIHYDRATE, (D-APT*2H2O), A NUCLEOSIDE TITLE 3 MONOPHOSPHATE WITH NEUTRAL PHOSPHODIESTER BACKBONE. AN X- TITLE 4 RAY CRYSTAL STUDY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP(CH3)*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS U-DNA, SINGLE STRAND, MODIFIED, OPEN EXPDTA X-RAY DIFFRACTION AUTHOR K.K.CHACKO,K.LINDNER,W.SAENGER,P.S.MILLER REVDAT 2 21-SEP-01 5 REVDAT 1 31-MAR-93 0 JRNL AUTH K.K.CHACKO,K.LINDNER,W.SAENGER,P.S.MILLER JRNL TITL MOLECULAR STRUCTURE OF JRNL TITL 2 DEOXYADENYLYL-3'-METHYLPHOSPHONATE-5'-THYMIDINE JRNL TITL 3 DIHYDRATE, (D-APT*2H2O), A NUCLEOSIDE JRNL TITL 4 MONOPHOSPHATE WITH NEUTRAL PHOSPHODIESTER JRNL TITL 5 BACKBONE. AN X-RAY CRYSTAL STUDY JRNL REF NUCLEIC ACIDS RES. V. 11 2801 1983 JRNL REFN ASTM NARHAD UK ISSN 0305-1048 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROM. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 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 : 2176 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) : 0.105 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 : 60 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 5 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 +T A 2 REMARK 103 N6 A A 1 AND O2 +T 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 : STOE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2176 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 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: ETHANOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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 1/2-X,1/2+Y,-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 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 4.81450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 10.44200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 4.81450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 10.44200 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 +T A 2 O2P 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 REMARK 500 O HOH 5 O HOH 6 1.24 SEQRES 1 A 2 A +T MODRES +T A 2 T THYMINE MODIFIED WITH CH3 FTNOTE 1 ATOMS O3* AND C2* OF THE THYMINE SUGAR, AND THE TWO WATER FTNOTE 1 MOLECULES ARE DISORDERED. HET CH3 A 2 1 HETNAM CH3 METHYL GROUP FORMUL 2 CH3 C1 H3 FORMUL 3 HOH *5(H2 O1) LINK C CH3 A 2 P +T A 2 CRYST1 9.629 20.884 14.173 90.00 90.00 90.00 P 21 21 2 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 0.103853 0.000000 0.000000 0.00000 SCALE2 0.000000 0.047884 0.000000 0.00000 SCALE3 0.000000 0.000000 0.070557 0.00000 ATOM 1 O5* A A 1 7.384 18.875 5.262 1.00 10.00 O ATOM 2 C5* A A 1 7.412 17.507 4.928 1.00 10.00 C ATOM 3 C4* A A 1 6.014 16.922 5.173 1.00 10.00 C ATOM 4 O4* A A 1 5.747 16.891 6.646 1.00 10.00 O ATOM 5 C3* A A 1 4.840 17.705 4.608 1.00 10.00 C ATOM 6 O3* A A 1 3.840 16.705 4.214 1.00 10.00 O ATOM 7 C2* A A 1 4.331 18.547 5.777 1.00 10.00 C ATOM 8 C1* A A 1 4.606 17.682 7.000 1.00 10.00 C ATOM 9 N9 A A 1 4.887 18.418 8.200 1.00 10.00 N ATOM 10 C8 A A 1 5.897 19.341 8.393 1.00 10.00 C ATOM 11 N7 A A 1 6.059 19.669 9.659 1.00 10.00 N ATOM 12 C5 A A 1 5.151 18.823 10.307 1.00 10.00 C ATOM 13 C6 A A 1 4.800 18.662 11.704 1.00 10.00 C ATOM 14 N6 A A 1 5.389 19.293 12.631 1.00 10.00 N ATOM 15 N1 A A 1 3.885 17.735 11.996 1.00 10.00 N ATOM 16 C2 A A 1 3.283 17.079 11.015 1.00 10.00 C ATOM 17 N3 A A 1 3.491 17.119 9.726 1.00 10.00 N ATOM 18 C4 A A 1 4.428 18.021 9.432 1.00 10.00 C ATOM 19 1H5* A A 1 8.176 17.052 5.581 1.00 10.00 H ATOM 20 2H5* A A 1 7.732 17.417 3.893 1.00 10.00 H ATOM 21 H4* A A 1 5.991 15.918 4.766 1.00 10.00 H ATOM 22 H3* A A 1 5.158 18.355 3.760 1.00 10.00 H ATOM 23 H1* A A 1 3.705 17.037 7.096 1.00 10.00 H ATOM 24 H8 A A 1 6.496 19.740 7.577 1.00 10.00 H ATOM 25 1H6 A A 1 6.137 20.218 12.610 1.00 10.00 H ATOM 26 2H6 A A 1 5.421 19.378 13.660 1.00 10.00 H ATOM 27 H2 A A 1 2.456 16.417 11.394 1.00 10.00 H ATOM 28 1H2* A A 1 4.973 19.531 5.832 1.00 10.00 H ATOM 29 2H2* A A 1 3.309 18.879 5.618 1.00 10.00 H ATOM 30 H5T A A 1 8.522 19.004 5.102 1.00 10.00 H ATOM 31 P +T A 2 2.712 16.991 3.156 1.00 10.00 P ATOM 32 O1P +T A 2 2.608 18.393 2.672 1.00 10.00 O ATOM 33 O5* +T A 2 3.006 16.003 2.042 1.00 10.00 O ATOM 34 C5* +T A 2 3.899 16.432 0.884 1.00 10.00 C ATOM 35 C4* +T A 2 4.446 15.095 0.274 1.00 10.00 C ATOM 36 O4* +T A 2 5.370 14.523 1.125 1.00 10.00 O ATOM 37 C3* +T A 2 3.412 13.982 -0.098 1.00 10.00 C ATOM 38 O3*A +T A 2 3.847 13.742 -1.551 0.65 10.00 O ATOM 39 O3*B +T A 2 2.764 13.863 -1.352 0.35 10.00 O ATOM 40 C2*A +T A 2 3.678 12.948 0.893 0.65 10.00 C ATOM 41 C2*B +T A 2 4.237 12.739 -0.071 0.35 10.00 C ATOM 42 C1* +T A 2 5.230 13.115 1.030 1.00 10.00 C ATOM 43 N1 +T A 2 5.408 12.585 2.443 1.00 10.00 N ATOM 44 C2 +T A 2 6.241 11.540 2.598 1.00 10.00 C ATOM 45 O2 +T A 2 6.747 10.956 1.697 1.00 10.00 O ATOM 46 N3 +T A 2 6.484 11.156 3.912 1.00 10.00 N ATOM 47 C4 +T A 2 5.926 11.770 5.056 1.00 10.00 C ATOM 48 O4 +T A 2 6.297 11.457 6.148 1.00 10.00 O ATOM 49 C5 +T A 2 5.005 12.858 4.823 1.00 10.00 C ATOM 50 C5M +T A 2 4.435 13.556 5.995 1.00 10.00 C ATOM 51 C6 +T A 2 4.807 13.205 3.539 1.00 10.00 C ATOM 52 1H5* +T A 2 4.679 17.106 1.178 1.00 10.00 H ATOM 53 2H5* +T A 2 3.258 16.981 0.086 1.00 10.00 H ATOM 54 H4* +T A 2 4.955 15.421 -0.690 1.00 10.00 H ATOM 55 H3* +T A 2 2.390 14.406 -0.027 1.00 10.00 H ATOM 56 1H2* +T A 2 3.065 13.322 1.670 1.00 10.00 H ATOM 57 2H2* +T A 2 3.246 12.173 0.309 1.00 10.00 H ATOM 58 H1* +T A 2 5.835 12.551 0.254 1.00 10.00 H ATOM 59 H3 +T A 2 7.181 10.461 4.116 1.00 10.00 H ATOM 60 H6 +T A 2 4.116 14.076 3.319 1.00 10.00 H TER 61 +T A 2 HETATM 62 C CH3 A 2 1.209 16.292 3.859 1.00 10.00 C HETATM 63 O HOH 3 0.482 19.435 5.502 0.60 10.00 O HETATM 64 O HOH 4 3.299 20.097 0.839 0.60 10.00 O HETATM 65 O HOH 5 6.761 19.499 2.137 0.30 10.00 O HETATM 66 O HOH 6 5.677 19.284 1.570 0.30 10.00 O HETATM 67 O HOH 7 0.936 20.577 2.684 0.20 10.00 O CONECT 31 62 CONECT 62 31 MASTER 217 1 1 0 0 0 0 6 66 1 2 1 END