HEADER DNA 06-AUG-98 1BPS TITLE MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF TITLE 2 DA IN DUPLEX DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*TP*CP*(BAP)AP*CP*GP*AP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY- COMPND 6 7,8,9,10- TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO COMPND 7 THE EXOCYCLIC N6 AMINO GROUP OF DEOXYADENOSINE IN THE COMPND 8 CENTER OF THE DUPLEX THROUGH TRANS ADDITION AT THE C10 OF COMPND 9 THE EPOXIDE.; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, BENZO[A]PYRENE DIOL EPOXIDE ADDUCT, KEYWDS 2 DUPLEX DNA EXPDTA SOLUTION NMR AUTHOR J.S.SCHWARTZ,J.S.RICE,B.A.LUXON,J.M.SAYER,G.XIE,H.J.C.YEH, AUTHOR 2 X.LIU,D.M.JERINA,D.G.GORENSTEIN REVDAT 5 24-FEB-09 1BPS 1 VERSN REVDAT 4 01-APR-03 1BPS 1 JRNL REVDAT 3 26-SEP-01 1BPS 3 ATOM CONECT REVDAT 2 29-DEC-99 1BPS 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 19-AUG-98 1BPS 0 JRNL AUTH J.L.SCHWARTZ,J.S.RICE,B.A.LUXON,J.M.SAYER,G.XIE, JRNL AUTH 2 H.J.YEH,X.LIU,D.M.JERINA,D.G.GORENSTEIN JRNL TITL SOLUTION STRUCTURE OF THE MINOR CONFORMER OF A DNA JRNL TITL 2 DUPLEX CONTAINING A DG MISMATCH OPPOSITE A JRNL TITL 3 BENZO[A]PYRENE DIOL EPOXIDE/DA ADDUCT: GLYCOSIDIC JRNL TITL 4 ROTATION FROM SYN TO ANTI AT THE MODIFIED JRNL TITL 5 DEOXYADENOSINE. JRNL REF BIOCHEMISTRY V. 36 11069 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9333324 JRNL DOI 10.1021/BI971306U REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 4.1 REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FOLLOWING RESTRAINTS WERE REMARK 3 APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION REMARK 3 CALCULATIONS: (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY REMARK 3 DERIVED FROM RELAXATION MATRIX ANALYSIS OF NOE DATA; (2) IMINO REMARK 3 PROTON HYDROGEN BOND RESTRAINTS FOR ALL BASE PAIRS EXCEPT THE REMARK 3 CENTRAL DA-DG MISMATCH PAIR. THE MODIFIED DA RESIDUE OF THIS REMARK 3 MINOR CONFORMER DISPLAYED A C2'-ENDO SUGAR PUCKER AND AN ANTI REMARK 3 GLYCOSIDIC BOND. IT FORMED AN ANTI:ANTI BASE PAIR CONTAINING REMARK 3 TWO HYDROGEN BONDS WITH THE OPPOSITE DG. THE MODIFIED DA REMARK 3 RESIDUE OF THE MAJOR CONFORMER OF THIS MOLECULE [YEH ET AL. REMARK 3 (1995) BIOCHEMISTRY 34, 13570-13581] DISPLAYED C3'-ENDO SUGAR REMARK 3 PUCKER AND A SYN GLYCOSIDIC BOND. THE MAJOR CONFORMER MODIFIED REMARK 3 DA RESIDUE FORMED A SYN:ANTI BASE PAIR CONTAINING NON-WATSON REMARK 3 CRICK HYDROGEN BONDS WITH THE OPPOSITE DG. MORE REFINEMENT REMARK 3 DETAILS CAN BE FOUND IN THE PRIMARY JOURNAL CITATION (SCHWARTZ REMARK 3 ET AL.,1997). REMARK 4 REMARK 4 1BPS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-99. REMARK 100 THE RCSB ID CODE IS RCSB008021. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 76 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, ROESY, TOCSY, AND 2D REMARK 210 EXCHANGE-ONLY SPECTRA REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS 750, 600 MHZ REMARK 210 SPECTROMETERS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MORASS 2.2, AMBER 4.1 REMARK 210 METHOD USED : RELAXATION MATRIX REFINEMENT REMARK 210 OF NOE DISTANCE RESTRAINTS AND REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 WITH SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS REMARK 210 DETERMINED USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY REMARK 210 EXPERIMENTS DONE IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D REMARK 210 ROESY, TOCSY, AND EXCHANGE-ONLY EXPERIMENTS WERE USED IN THE REMARK 210 CHEMICAL SHIFT ASSIGNMENT PROCESS. 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 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT B 11 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES 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 DC A 4 0.16 SIDE_CHAIN REMARK 500 DA A 5 0.08 SIDE_CHAIN REMARK 500 DG B 13 0.12 SIDE_CHAIN REMARK 500 DA B 16 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BAP A 10 DBREF 1BPS A 1 9 PDB 1BPS 1BPS 1 9 DBREF 1BPS B 10 18 PDB 1BPS 1BPS 10 18 SEQRES 1 A 9 DG DG DT DC DA DC DG DA DG SEQRES 1 B 9 DC DT DC DG DG DG DA DC DC HET BAP A 10 38 HETNAM BAP 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE FORMUL 3 BAP C20 H16 O3 LINK N6 DA A 5 C4' BAP A 10 1555 1555 1.47 SITE 1 AC1 5 DC A 4 DA A 5 DC A 6 DG B 13 SITE 2 AC1 5 DG B 14 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 MASTER 124 0 1 0 0 0 2 6 0 0 0 2 END