HEADER DEOXYRIBONUCLEIC ACID 24-SEP-02 1MV7 OBSLTE 25-MAY-04 1MV7 1SM5 TITLE CRYSTAL STRUCTURE OF A DNA DECAMER CONTAINING A THYMINE- TITLE 2 DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*(BRO)UP*TP*AP*AP*TP*(BRO)UP*CP*G)-3'; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS UV-DAMAGED DNA, THYMINE DIMER, DNA DECAMER EXPDTA X-RAY DIFFRACTION AUTHOR H.PARK,K.ZHANG,Y.REN,S.NADJI,N.SINHA,J.-S.TAYLOR,C.KANG REVDAT 2 25-MAY-04 1MV7 1 OBSLTE REVDAT 1 13-DEC-02 1MV7 0 JRNL AUTH H.PARK,K.ZHANG,Y.REN,S.NADJI,N.SINHA,J.-S.TAYLOR, JRNL AUTH 2 C.KANG JRNL TITL CRYSTAL STRUCTURE OF A DNA DECAMER CONTAINING A JRNL TITL 2 CYS-SYN THYMINE-DIMER JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 15965 2002 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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 : 6447 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 372 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 19 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 : 804 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 52 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) : 0.023 REMARK 3 BOND ANGLES (DEGREES) : 1.35 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 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 1MV7 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 14-OCT-2002. REMARK 100 THE NDB ID CODE IS BD0058. REMARK 101 REMARK 101 RESIDUE +U A 3 HAS BRO BONDED TO C5. REMARK 101 RESIDUE +U A 8 HAS BRO BONDED TO C5. REMARK 101 RESIDUE +U C 103 HAS BRO BONDED TO C5. REMARK 101 RESIDUE +U C 108 HAS BRO BONDED TO C5. 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 : 03-DEC-2001 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : 9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9205, 0.8434, 0.9207 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUN-315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7865 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGCL2, HEPES-NA, PEG 400, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 12.25000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.66500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.92500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.66500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.92500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 4 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 C6 T B 15 C5 T B 16 1.86 REMARK 500 C6 T D 115 C5 T D 116 1.87 REMARK 500 C5 T B 15 C6 T B 16 2.12 REMARK 500 C5 T D 115 C6 T D 116 2.13 REMARK 500 C5 T B 15 C4 T B 16 2.18 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 218 DISTANCE = 7.68 ANGSTROMS REMARK 525 HOH 219 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH 220 DISTANCE = 11.36 ANGSTROMS REMARK 525 HOH 228 DISTANCE = 8.86 ANGSTROMS REMARK 525 HOH 229 DISTANCE = 12.79 ANGSTROMS REMARK 525 HOH 245 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH 246 DISTANCE = 10.43 ANGSTROMS SEQRES 1 A 10 G C +U T A A T +U C G SEQRES 1 B 10 C G A A T T A A G C SEQRES 1 C 10 G C +U T A A T +U C G SEQRES 1 D 10 C G A A T T A A G C HET BRO A 3 1 HET BRO A 8 1 HET BRO C 103 1 HET BRO C 108 1 HETNAM BRO BROMO GROUP FORMUL 5 BRO 4(BR) FORMUL 9 HOH *52(H2 O1) LINK BR BRO A 3 C5 +U A 3 LINK BR BRO A 8 C5 +U A 8 LINK C5 T B 15 C5 T B 16 LINK C6 T B 15 C6 T B 16 LINK C5 T D 115 C5 T D 116 LINK C6 T D 115 C6 T D 116 LINK BR BRO C 103 C5 +U C 103 LINK BR BRO C 108 C5 +U C 108 CRYST1 24.500 53.850 75.330 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 0.040816 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018570 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013275 0.00000 TER 200 G A 10 HETATM 201 BR BRO A 3 23.101 31.727 46.927 1.00 41.61 BR HETATM 202 BR BRO A 8 9.576 21.253 55.494 1.00 38.00 BR TER 406 C B 20 TER 606 G C 110 HETATM 607 BR BRO C 103 18.101 31.821 25.418 1.00 38.28 BR HETATM 608 BR BRO C 108 26.837 18.784 36.514 1.00 34.72 BR TER 812 C D 120 HETATM 813 O HOH 201 19.408 25.863 46.707 1.00 39.74 O HETATM 814 O HOH 202 13.288 18.610 25.239 1.00 33.46 O HETATM 815 O HOH 203 16.842 43.530 51.744 1.00 26.58 O HETATM 816 O HOH 204 18.714 44.460 26.526 1.00 26.05 O HETATM 817 O HOH 205 14.643 16.119 24.109 1.00 38.69 O HETATM 818 O HOH 206 24.789 29.258 49.140 1.00 16.97 O HETATM 819 O HOH 207 27.899 21.155 39.327 1.00 33.73 O HETATM 820 O HOH 208 10.818 11.474 55.646 1.00 26.36 O HETATM 821 O HOH 209 13.051 29.028 62.914 1.00 25.93 O HETATM 822 O HOH 210 14.049 27.072 42.428 1.00 23.54 O HETATM 823 O HOH 211 15.608 40.111 23.912 1.00 14.17 O HETATM 824 O HOH 212 26.410 25.270 30.040 1.00 36.08 O HETATM 825 O HOH 213 20.975 4.041 36.728 1.00 35.12 O HETATM 826 O HOH 214 18.010 22.884 48.094 1.00 38.66 O HETATM 827 O HOH 215 24.708 26.738 28.323 1.00 38.72 O HETATM 828 O HOH 216 27.830 10.498 35.274 1.00 26.08 O HETATM 829 O HOH 217 23.076 8.712 38.526 1.00 22.53 O HETATM 830 O HOH 218 33.711 25.192 31.234 1.00 33.67 O HETATM 831 O HOH 219 11.022 21.926 24.902 1.00 20.18 O HETATM 832 O HOH 220 7.210 27.387 70.552 1.00 25.76 O HETATM 833 O HOH 221 12.754 23.925 30.487 1.00 29.45 O HETATM 834 O HOH 222 2.901 28.194 52.192 1.00 33.25 O HETATM 835 O HOH 223 17.118 12.557 24.778 1.00 24.44 O HETATM 836 O HOH 224 21.634 36.365 54.828 1.00 33.15 O HETATM 837 O HOH 225 20.766 15.898 43.071 1.00 29.33 O HETATM 838 O HOH 226 16.643 8.137 33.427 1.00 30.59 O HETATM 839 O HOH 227 21.709 19.168 20.762 1.00 24.34 O HETATM 840 O HOH 228 0.999 33.198 37.948 1.00 30.92 O HETATM 841 O HOH 229 0.247 25.777 68.944 1.00 32.56 O HETATM 842 O HOH 230 14.958 32.626 61.217 1.00 23.19 O HETATM 843 O HOH 231 19.579 40.223 26.515 1.00 19.68 O HETATM 844 O HOH 232 18.582 5.175 36.110 1.00 41.02 O HETATM 845 O HOH 233 26.350 42.892 38.721 1.00 24.95 O HETATM 846 O HOH 234 18.921 45.529 57.758 1.00 24.17 O HETATM 847 O HOH 235 34.126 30.879 49.421 1.00 24.23 O HETATM 848 O HOH 236 18.885 17.535 55.466 1.00 35.14 O HETATM 849 O HOH 237 11.885 32.054 50.308 1.00 24.33 O HETATM 850 O HOH 238 13.636 31.612 31.399 1.00 26.94 O HETATM 851 O HOH 239 13.652 10.366 55.372 1.00 30.96 O HETATM 852 O HOH 240 20.887 40.066 29.022 1.00 40.51 O HETATM 853 O HOH 241 33.194 27.995 48.436 1.00 23.57 O HETATM 854 O HOH 242 7.481 25.453 48.806 1.00 28.18 O HETATM 855 O HOH 243 19.116 20.316 24.342 1.00 14.02 O HETATM 856 O HOH 244 21.435 6.004 38.910 1.00 36.46 O HETATM 857 O HOH 245 33.271 31.214 54.561 1.00 26.67 O HETATM 858 O HOH 246 19.562 7.372 17.085 1.00 24.63 O HETATM 859 O HOH 247 6.408 9.885 42.884 1.00 21.93 O HETATM 860 O HOH 248 21.542 24.325 27.255 1.00 34.54 O HETATM 861 O HOH 249 18.301 25.711 36.254 1.00 35.79 O HETATM 862 O HOH 250 17.708 34.651 55.289 1.00 23.02 O HETATM 863 O HOH 251 12.943 21.632 38.533 1.00 20.76 O HETATM 864 O HOH 252 6.487 14.841 53.290 1.00 17.23 O CONECT 56 201 CONECT 157 202 CONECT 201 56 CONECT 202 157 CONECT 300 320 CONECT 302 322 CONECT 320 300 CONECT 322 302 CONECT 462 607 CONECT 563 608 CONECT 607 462 CONECT 608 563 CONECT 706 726 CONECT 708 728 CONECT 726 706 CONECT 728 708 MASTER 242 0 4 0 0 0 0 6 860 4 16 4 END