HEADER DNA 30-MAY-03 1PIB TITLE SOLUTION STRUCTURE OF DNA CONTAINING CPD OPPOSITED BY GA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*AP*TP*TP*AP*CP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*GP*TP*GP*AP*TP*GP*CP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS CIS-SYN CYCLOBUTANE PYRIMIDINE DIMER, CPD CONTAINING DNA, HELICAL KEYWDS 2 DISTORTION, THYMINEDIMER, DNA EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR J.H.LEE,C.J.PARK,J.S.SHIN,B.S.CHOI REVDAT 3 23-FEB-22 1PIB 1 REMARK LINK REVDAT 2 24-FEB-09 1PIB 1 VERSN REVDAT 1 18-MAY-04 1PIB 0 JRNL AUTH J.H.LEE,C.J.PARK,J.S.SHIN,T.IKEGAMI,H.AKUTSU,B.S.CHOI JRNL TITL NMR STRUCTURE OF THE DNA DECAMER DUPLEX CONTAINING DOUBLE JRNL TITL 2 T*G MISMATCHES OF CIS-SYN CYCLOBUTANE PYRIMIDINE DIMER: JRNL TITL 3 IMPLICATIONS FOR DNA DAMAGE RECOGNITION BY THE XPC-HHR23B JRNL TITL 4 COMPLEX. JRNL REF NUCLEIC ACIDS RES. V. 32 2474 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 15121904 JRNL DOI 10.1093/NAR/GKH568 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR 3.1 REMARK 3 AUTHORS : FRANK DELAGLIO (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PIB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019339. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277; 300; 290 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 100MM NACL; 100MM NACL; 100MM REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM DNA, 20MM PHOSPHATE BUFFER; REMARK 210 1MM DNA, 20MM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1, SPARKY 3.106 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DA A 4 N9 DA A 4 C4 0.045 REMARK 500 1 DT A 5 N1 DT A 5 C2 0.069 REMARK 500 1 DT A 5 C2 DT A 5 N3 0.050 REMARK 500 1 DT A 5 C4 DT A 5 C5 0.085 REMARK 500 1 DT A 5 C5 DT A 5 C6 0.255 REMARK 500 1 DT A 6 N1 DT A 6 C2 0.058 REMARK 500 1 DT A 6 C4 DT A 6 C5 0.072 REMARK 500 1 DT A 6 C5 DT A 6 C6 0.237 REMARK 500 1 DT A 6 C6 DT A 6 N1 0.061 REMARK 500 2 DA A 4 N9 DA A 4 C4 0.044 REMARK 500 2 DT A 5 N1 DT A 5 C2 0.069 REMARK 500 2 DT A 5 C4 DT A 5 C5 0.081 REMARK 500 2 DT A 5 C5 DT A 5 C6 0.256 REMARK 500 2 DT A 6 N1 DT A 6 C2 0.060 REMARK 500 2 DT A 6 C4 DT A 6 C5 0.069 REMARK 500 2 DT A 6 C5 DT A 6 C6 0.245 REMARK 500 2 DT A 6 C6 DT A 6 N1 0.065 REMARK 500 2 DT B 17 N1 DT B 17 C2 0.049 REMARK 500 3 DA A 4 N9 DA A 4 C4 0.045 REMARK 500 3 DT A 5 N1 DT A 5 C2 0.075 REMARK 500 3 DT A 5 C2 DT A 5 N3 0.056 REMARK 500 3 DT A 5 C4 DT A 5 C5 0.080 REMARK 500 3 DT A 5 C5 DT A 5 C6 0.258 REMARK 500 3 DT A 5 C5 DT A 5 C7 0.037 REMARK 500 3 DT A 6 N1 DT A 6 C2 0.058 REMARK 500 3 DT A 6 C4 DT A 6 C5 0.070 REMARK 500 3 DT A 6 C5 DT A 6 C6 0.239 REMARK 500 3 DT A 6 C6 DT A 6 N1 0.063 REMARK 500 3 DT B 17 N1 DT B 17 C2 0.052 REMARK 500 4 DA A 4 N9 DA A 4 C4 0.041 REMARK 500 4 DT A 5 N1 DT A 5 C2 0.068 REMARK 500 4 DT A 5 C2 DT A 5 N3 0.050 REMARK 500 4 DT A 5 C4 DT A 5 C5 0.086 REMARK 500 4 DT A 5 C5 DT A 5 C6 0.257 REMARK 500 4 DT A 6 N1 DT A 6 C2 0.059 REMARK 500 4 DT A 6 C4 DT A 6 C5 0.072 REMARK 500 4 DT A 6 C5 DT A 6 C6 0.237 REMARK 500 4 DT A 6 C6 DT A 6 N1 0.060 REMARK 500 5 DA A 4 N9 DA A 4 C4 0.039 REMARK 500 5 DT A 5 N1 DT A 5 C2 0.069 REMARK 500 5 DT A 5 C2 DT A 5 N3 0.053 REMARK 500 5 DT A 5 C4 DT A 5 C5 0.082 REMARK 500 5 DT A 5 C5 DT A 5 C6 0.255 REMARK 500 5 DT A 6 N1 DT A 6 C2 0.061 REMARK 500 5 DT A 6 C4 DT A 6 C5 0.068 REMARK 500 5 DT A 6 C5 DT A 6 C6 0.237 REMARK 500 5 DT A 6 C6 DT A 6 N1 0.063 REMARK 500 6 DA A 4 N9 DA A 4 C4 0.043 REMARK 500 6 DT A 5 N1 DT A 5 C2 0.071 REMARK 500 6 DT A 5 C2 DT A 5 N3 0.055 REMARK 500 REMARK 500 THIS ENTRY HAS 149 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 DG A 2 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 2 C3' - O3' - P ANGL. DEV. = 14.2 DEGREES REMARK 500 1 DC A 3 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 1 DA A 4 C3' - O3' - P ANGL. DEV. = 13.5 DEGREES REMARK 500 1 DT A 5 C4 - C5 - C6 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DT A 5 C4 - C5 - C7 ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DT A 5 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DT A 6 C5 - C6 - N1 ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -16.3 DEGREES REMARK 500 1 DT A 6 C3' - O3' - P ANGL. DEV. = 14.6 DEGREES REMARK 500 1 DC A 8 C3' - O3' - P ANGL. DEV. = 14.9 DEGREES REMARK 500 1 DG A 9 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 9 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES REMARK 500 1 DG B 11 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DC B 12 P - O5' - C5' ANGL. DEV. = 9.8 DEGREES REMARK 500 1 DC B 12 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES REMARK 500 1 DG B 13 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DT B 14 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES REMARK 500 1 DG B 15 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DG B 15 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES REMARK 500 1 DA B 16 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 1 DT B 17 C3' - O3' - P ANGL. DEV. = 13.2 DEGREES REMARK 500 1 DG B 18 P - O5' - C5' ANGL. DEV. = 10.5 DEGREES REMARK 500 1 DG B 18 N3 - C2 - N2 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 18 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES REMARK 500 1 DC B 19 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 1 DG B 20 N3 - C2 - N2 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 DG A 2 N3 - C2 - N2 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG A 2 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES REMARK 500 2 DC A 3 P - O5' - C5' ANGL. DEV. = 9.9 DEGREES REMARK 500 2 DC A 3 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 2 DA A 4 C3' - O3' - P ANGL. DEV. = 11.4 DEGREES REMARK 500 2 DT A 5 C4 - C5 - C6 ANGL. DEV. = -6.5 DEGREES REMARK 500 2 DT A 5 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT A 5 C4 - C5 - C7 ANGL. DEV. = -9.8 DEGREES REMARK 500 2 DT A 5 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DT A 6 C5 - C6 - N1 ANGL. DEV. = -7.7 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -14.9 DEGREES REMARK 500 2 DT A 6 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 2 DA A 7 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 2 DC A 8 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES REMARK 500 2 DG A 9 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DG A 9 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 2 DG B 11 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DC B 12 P - O5' - C5' ANGL. DEV. = 9.6 DEGREES REMARK 500 2 DC B 12 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES REMARK 500 2 DG B 13 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 2 DT B 14 C3' - O3' - P ANGL. DEV. = 12.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 479 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DT A 5 0.09 SIDE CHAIN REMARK 500 1 DT A 6 0.33 SIDE CHAIN REMARK 500 2 DT A 5 0.09 SIDE CHAIN REMARK 500 2 DT A 6 0.29 SIDE CHAIN REMARK 500 3 DT A 5 0.08 SIDE CHAIN REMARK 500 3 DT A 6 0.33 SIDE CHAIN REMARK 500 4 DT A 5 0.09 SIDE CHAIN REMARK 500 4 DT A 6 0.34 SIDE CHAIN REMARK 500 5 DT A 5 0.09 SIDE CHAIN REMARK 500 5 DT A 6 0.33 SIDE CHAIN REMARK 500 6 DT A 5 0.09 SIDE CHAIN REMARK 500 6 DT A 6 0.33 SIDE CHAIN REMARK 500 7 DT A 5 0.08 SIDE CHAIN REMARK 500 7 DT A 6 0.28 SIDE CHAIN REMARK 500 8 DT A 5 0.09 SIDE CHAIN REMARK 500 8 DT A 6 0.34 SIDE CHAIN REMARK 500 9 DT A 5 0.09 SIDE CHAIN REMARK 500 9 DT A 6 0.32 SIDE CHAIN REMARK 500 10 DT A 5 0.08 SIDE CHAIN REMARK 500 10 DT A 6 0.31 SIDE CHAIN REMARK 500 11 DT A 5 0.09 SIDE CHAIN REMARK 500 11 DT A 6 0.32 SIDE CHAIN REMARK 500 12 DT A 5 0.08 SIDE CHAIN REMARK 500 12 DT A 6 0.31 SIDE CHAIN REMARK 500 13 DT A 5 0.09 SIDE CHAIN REMARK 500 13 DT A 6 0.33 SIDE CHAIN REMARK 500 14 DT A 5 0.09 SIDE CHAIN REMARK 500 14 DT A 6 0.29 SIDE CHAIN REMARK 500 15 DT A 5 0.09 SIDE CHAIN REMARK 500 15 DT A 6 0.27 SIDE CHAIN REMARK 500 16 DT A 5 0.08 SIDE CHAIN REMARK 500 16 DT A 6 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SNH RELATED DB: PDB REMARK 900 REFERRED TO AS THE CPD/GG DUPLEX DBREF 1PIB A 1 10 PDB 1PIB 1PIB 1 10 DBREF 1PIB B 11 20 PDB 1PIB 1PIB 11 20 SEQRES 1 A 10 DC DG DC DA DT DT DA DC DG DC SEQRES 1 B 10 DG DC DG DT DG DA DT DG DC DG LINK C5 DT A 5 C5 DT A 6 1555 1555 1.65 LINK C6 DT A 5 C6 DT A 6 1555 1555 1.64 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1