HEADER DEOXYRIBONUCLEIC ACID 11-SEP-95 UDBA41 TITLE MOLECULAR AND CRYSTAL STRUCTURE OF SP-THYMIDIN-3'-YL 4- TITLE 2 THIOTHYMIDIN-5'-YL METHYLPHOSPHONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP(CH3)*(S)T)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS U-DNA, SINGLE STRAND EXPDTA X-RAY DIFFRACTION AUTHOR T.SZABO,D.NOREUS,R.NORRESTAM,J.STAWINSKI REVDAT 2 21-SEP-01 5 REVDAT 1 11-SEP-95 0 JRNL AUTH T.SZABO,D.NOREUS,R.NORRESTAM,J.STAWINSKI JRNL TITL MOLECULAR AND CRYSTAL STRUCTURE OF JRNL TITL 2 SP-THYMIDIN-3'-YL 4-THIOTHYMIDIN-5'-YL JRNL TITL 3 METHYLPHOSPHONATE JRNL REF NUCLEIC ACIDS RES. V. 21 3921 1993 JRNL REFN ASTM NARHAD UK ISSN 0305-1048 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NULL ANGSTROM. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : NULL 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 : 1237 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) : 0.058 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 : 35 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 2 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 101 REMARK 101 RESIDUE +T A 2 HAS S BONDED TO C4. 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) : 173.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL 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: NULL 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 6.62050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 7.47200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 6.92200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 7.47200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 6.62050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 6.92200 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 O4 SEQRES 1 A 2 +T +T MODRES +T A 2 T THYMINE MODIFIED WITH CH3-S HET CH3 A 2 1 HET S A 2 1 HET MOH 3 2 HETNAM CH3 METHYL GROUP HETNAM S SULFUR ATOM HETNAM MOH METHANOL FORMUL 2 CH3 C1 H3 FORMUL 3 S S1 FORMUL 4 MOH C1 H4 O1 LINK S S A 2 C4 +T A 2 LINK C CH3 A 2 P +T A 2 CRYST1 13.241 13.844 14.944 90.00 90.00 90.00 P 21 21 21 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 0.075523 0.000000 0.000000 0.00000 SCALE2 0.000000 0.072233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.066916 0.00000 ATOM 1 O5* T A 1 8.333 2.824 6.900 10.00 3.16 O ATOM 2 C5* T A 1 8.060 1.815 5.880 10.00 3.32 C ATOM 3 C4* T A 1 6.583 1.696 5.582 10.00 1.42 C ATOM 4 O4* T A 1 5.886 1.060 6.710 10.00 2.05 O ATOM 5 C3* T A 1 5.894 3.040 5.369 10.00 2.05 C ATOM 6 O3* T A 1 4.935 2.935 4.252 10.00 1.66 O ATOM 7 C2* T A 1 5.119 3.346 6.665 10.00 1.89 C ATOM 8 C1* T A 1 4.939 1.944 7.303 10.00 2.13 C ATOM 9 N1 T A 1 5.224 1.962 8.793 10.00 1.26 N ATOM 10 C2 T A 1 4.136 2.056 9.673 10.00 1.97 C ATOM 11 O2 T A 1 2.988 2.115 9.297 10.00 2.21 O ATOM 12 N3 T A 1 4.520 2.120 10.985 10.00 1.42 N ATOM 13 C4 T A 1 5.796 2.162 11.510 10.00 1.58 C ATOM 14 O4 T A 1 5.956 2.262 12.723 10.00 2.05 O ATOM 15 C5 T A 1 6.847 2.006 10.544 10.00 1.82 C ATOM 16 C5M T A 1 8.359 1.964 11.008 10.00 2.53 C ATOM 17 C6 T A 1 6.526 1.946 9.238 10.00 1.58 C ATOM 18 P +T A 2 5.484 3.350 2.845 10.00 1.82 P ATOM 19 O1P +T A 2 6.873 2.892 2.585 10.00 2.29 O ATOM 20 O5* +T A 2 4.416 2.715 1.899 10.00 2.53 O ATOM 21 C5* +T A 2 4.765 1.765 0.853 10.00 2.21 C ATOM 22 C4* +T A 2 3.564 1.551 -0.048 10.00 1.89 C ATOM 23 O4* +T A 2 2.529 0.885 0.671 10.00 1.42 O ATOM 24 C3* +T A 2 2.951 2.866 -0.665 10.00 1.74 C ATOM 25 O3* +T A 2 2.492 2.502 -1.982 10.00 1.42 O ATOM 26 C2* +T A 2 1.770 3.075 0.263 10.00 1.50 C ATOM 27 C1* +T A 2 1.321 1.649 0.556 10.00 1.74 C ATOM 28 N1 +T A 2 0.564 1.501 1.829 10.00 1.42 N ATOM 29 C2 +T A 2 -0.809 1.469 1.728 10.00 1.26 C ATOM 30 O2 +T A 2 -1.410 1.503 0.666 10.00 2.21 O ATOM 31 N3 +T A 2 -1.447 1.377 2.922 10.00 1.42 N ATOM 32 C4 +T A 2 -0.826 1.376 4.172 10.00 2.21 C ATOM 33 C5 +T A 2 0.592 1.423 4.177 10.00 1.58 C ATOM 34 C5M +T A 2 1.341 1.382 5.474 10.00 2.61 C ATOM 35 C6 +T A 2 1.194 1.492 3.029 10.00 1.89 C TER 36 +T A 2 HETATM 37 C CH3 A 2 5.277 5.135 2.714 10.00 2.61 C HETATM 38 S S A 2 -1.793 1.290 5.538 10.00 2.61 S HETATM 39 C MOH 3 8.726 0.223 1.260 10.00 3.95 C HETATM 40 O MOH 3 8.931 0.946 2.494 10.00 2.92 O CONECT 18 37 CONECT 32 38 CONECT 37 18 CONECT 38 32 CONECT 39 40 CONECT 40 39 MASTER 208 0 3 0 0 0 0 6 39 1 6 1 END