HEADER DEOXYRIBONUCLEIC ACID 18-AUG-88 UDB007 TITLE MOLECULAR STRUCTURE OF A DEOXYRIBOSE-DINUCLEOTIDE, SODIUM TITLE 2 THYMIDYLYL-(5'-3')-THYMIDYLATE-(5') HYDRATE (PTPT), AND A TITLE 3 POSSIBLE STRUCTURAL MODEL FOR POLYTHYMIDYLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS U-DNA, SINGLE STRAND, OPEN EXPDTA X-RAY DIFFRACTION AUTHOR N.CAMERMAN,J.K.FAWCETT,A.CAMERMAN REVDAT 2 21-SEP-01 5 REVDAT 1 18-AUG-88 0 JRNL AUTH N.CAMERMAN,J.K.FAWCETT,A.CAMERMAN JRNL TITL MOLECULAR STRUCTURE OF A DEOXYRIBOSE-DINUCLEOTIDE, JRNL TITL 2 SODIUM THYMIDYLYL-(5'-3')-THYMIDYLATE-(5') HYDRATE JRNL TITL 3 (PTPT), AND A POSSIBLE STRUCTURAL MODEL FOR JRNL TITL 4 POLYTHYMIDYLATE JRNL REF J.MOL.BIOL. V. 107 601 1976 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.CAMERMAN,J.K.FAWCETT,A.CAMERMAN REMARK 1 TITL STRUCTURE OF A DINUCLEOTIDE: REMARK 1 TITL 2 THYMIDYLYL-(5'-3')-THYMIDYLYL-5' (PTPT). REMARK 1 REF SCIENCE V. 182 1142 1973 REMARK 1 REFN ASTM SCIEAS US ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 1.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 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 : 971 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) : 0.109 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 : 41 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 15 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 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 : 6.40 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 : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 971 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 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 (%): 36.1 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 8.03000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 7.56500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 8.03000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 7.56500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA 4 LIES ON A SPECIAL POSITION. REMARK 375 HOH 10 LIES ON A SPECIAL POSITION. REMARK 375 HOH 11 LIES ON A SPECIAL POSITION. 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 18 O HOH 19 1.72 SEQRES 1 A 2 T T FTNOTE 1 THIS SODIUM ION AND SOME WATERS ARE DISORDERED HET NA 3 1 HET NA 4 3 HETNAM NA SODIUM ION FORMUL 2 NA 2(NA1 1+) FORMUL 4 HOH *15(H2 O1) CRYST1 16.060 15.130 15.650 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 0.062267 0.000000 0.000000 0.00000 SCALE2 0.000000 0.066094 0.000000 0.00000 SCALE3 0.000000 0.000000 0.063898 0.00000 ATOM 1 O3P T A 1 6.347 4.097 1.321 1.00 10.00 O ANISOU 1 O3P T A 1 670 1110 1550 -100 180 -150 O ATOM 2 P T A 1 5.298 5.173 1.542 1.00 10.00 P ANISOU 2 P T A 1 440 640 540 -170 80 -30 P ATOM 3 O1P T A 1 5.859 6.344 2.227 1.00 10.00 O ANISOU 3 O1P T A 1 580 760 390 -340 70 230 O ATOM 4 O2P T A 1 4.572 5.391 0.227 1.00 10.00 O ANISOU 4 O2P T A 1 1000 2030 790 -750 -280 630 O ATOM 5 O5* T A 1 4.296 4.497 2.604 1.00 10.00 O ANISOU 5 O5* T A 1 240 890 440 -300 40 190 O ATOM 6 C5* T A 1 3.329 3.537 2.189 1.00 3.60 C ATOM 7 C4* T A 1 2.631 2.981 3.413 1.00 3.40 C ATOM 8 O4* T A 1 3.577 2.168 4.188 1.00 3.60 O ATOM 9 C3* T A 1 2.231 4.052 4.467 1.00 4.30 C ATOM 10 O3* T A 1 0.984 3.518 5.100 1.00 10.00 O ANISOU 10 O3* T A 1 170 460 460 -50 80 150 O ATOM 11 C2* T A 1 3.318 4.118 5.431 1.00 2.10 C ATOM 12 C1* T A 1 3.740 2.681 5.498 1.00 3.80 C ATOM 13 N1 T A 1 5.223 2.481 5.794 1.00 2.90 N ATOM 14 C2 T A 1 5.505 2.233 7.035 1.00 3.10 C ATOM 15 O2 T A 1 4.733 2.130 7.985 1.00 3.20 O ATOM 16 N3 T A 1 6.850 1.870 7.307 1.00 3.40 N ATOM 17 C4 T A 1 7.844 1.826 6.274 1.00 4.80 C ATOM 18 O4 T A 1 9.006 1.413 6.697 1.00 6.40 O ATOM 19 C5 T A 1 7.433 2.094 5.003 1.00 4.60 C ATOM 20 C5M T A 1 8.509 2.044 3.963 1.00 5.50 C ATOM 21 C6 T A 1 6.122 2.555 4.817 1.00 3.50 C ATOM 22 P T A 2 -0.427 4.138 4.737 1.00 10.00 P ANISOU 22 P T A 2 200 470 380 -10 -70 20 P ATOM 23 O1P T A 2 -0.527 4.273 3.277 1.00 10.00 O ANISOU 23 O1P T A 2 700 330 670 -180 -10 -100 O ATOM 24 O2P T A 2 -0.737 5.350 5.476 1.00 10.00 O ANISOU 24 O2P T A 2 180 460 720 110 -280 -130 O ATOM 25 O5* T A 2 -1.373 2.990 5.299 1.00 10.00 O ANISOU 25 O5* T A 2 300 350 440 -230 -260 20 O ATOM 26 C5* T A 2 -1.315 1.717 4.640 1.00 6.30 C ATOM 27 C4* T A 2 -2.380 0.744 5.263 1.00 3.70 C ATOM 28 O4* T A 2 -1.884 0.260 6.457 1.00 3.50 O ATOM 29 C3* T A 2 -3.755 1.548 5.523 1.00 4.20 C ATOM 30 O3* T A 2 -4.781 0.527 5.424 1.00 4.50 O ATOM 31 C2* T A 2 -3.577 1.855 7.022 1.00 3.10 C ATOM 32 C1* T A 2 -2.706 0.769 7.601 1.00 4.90 C ATOM 33 N1 T A 2 -1.800 1.200 8.642 1.00 4.20 N ATOM 34 C2 T A 2 -2.088 0.927 9.964 1.00 3.70 C ATOM 35 O2 T A 2 -3.154 0.330 10.265 1.00 3.70 O ATOM 36 N3 T A 2 -1.214 1.294 10.834 1.00 3.30 N ATOM 37 C4 T A 2 -0.022 1.866 10.606 1.00 3.90 C ATOM 38 O4 T A 2 0.824 2.133 11.528 1.00 4.90 O ATOM 39 C5 T A 2 0.283 2.148 9.233 1.00 3.60 C ATOM 40 C5M T A 2 1.685 2.790 8.786 1.00 6.10 C ATOM 41 C6 T A 2 -0.536 1.802 8.365 1.00 4.50 C TER 42 T A 2 HETATM 43 NA NA 3 -2.896 6.526 5.407 1.00 4.70 NA HETATM 44 NA A NA 4 1.421 1.465 0.091 0.50 9.00 NA HETATM 45 NA B NA 4 8.030 0.000 -0.023 0.25 13.20 NA HETATM 46 NA C NA 4 -4.264 7.179 2.823 0.25 5.90 NA HETATM 47 O HOH 5 1.595 6.890 6.382 1.00 4.30 O HETATM 48 O HOH 6 7.802 4.984 14.536 1.00 10.30 O HETATM 49 O HOH 7 3.188 7.358 13.123 1.00 7.20 O HETATM 50 O HOH 8 0.975 2.875 14.179 1.00 11.80 O HETATM 51 O HOH 9 3.713 2.524 11.498 1.00 8.40 O HETATM 52 O HOH 10 8.030 7.565 1.138 1.00 7.50 O HETATM 53 O HOH 11 8.030 7.565 13.700 1.00 20.80 O HETATM 54 O HOH 12 2.642 7.532 3.222 0.75 7.40 O HETATM 55 O HOH 13 2.239 5.420 14.745 0.75 13.10 O HETATM 56 O HOH 14 6.183 1.443 0.828 1.00 11.70 O HETATM 57 O HOH 15 3.464 1.247 14.357 0.75 14.10 O HETATM 58 O HOH 16 2.484 0.089 1.258 1.00 14.60 O HETATM 59 O HOH 17 4.818 3.707 13.756 1.00 18.50 O HETATM 60 O HOH 18 0.652 6.403 1.831 0.75 15.90 O HETATM 61 O HOH 19 1.193 5.984 0.257 0.25 18.80 O MASTER 224 1 2 0 0 0 0 6 60 1 0 1 END