HEADER DNA 06-AUG-98 1BPS TITLE MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN TITLE 2 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-7,8,9,10- COMPND 6 TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6 COMPND 7 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH COMPND 8 TRANS ADDITION AT THE C10 OF THE EPOXIDE.; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS DEOXYRIBONUCLEIC ACID, BENZO[A]PYRENE DIOL EPOXIDE ADDUCT, DUPLEX KEYWDS 2 DNA, DNA EXPDTA SOLUTION NMR AUTHOR J.S.SCHWARTZ,J.S.RICE,B.A.LUXON,J.M.SAYER,G.XIE,H.J.C.YEH,X.LIU, AUTHOR 2 D.M.JERINA,D.G.GORENSTEIN REVDAT 7 27-DEC-23 1BPS 1 REMARK REVDAT 6 03-NOV-21 1BPS 1 SOURCE REMARK LINK 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,H.J.YEH, JRNL AUTH 2 X.LIU,D.M.JERINA,D.G.GORENSTEIN JRNL TITL SOLUTION STRUCTURE OF THE MINOR CONFORMER OF A DNA DUPLEX JRNL TITL 2 CONTAINING A DG MISMATCH OPPOSITE A BENZO[A]PYRENE DIOL JRNL TITL 3 EPOXIDE/DA ADDUCT: GLYCOSIDIC ROTATION FROM SYN TO ANTI AT JRNL TITL 4 THE MODIFIED DEOXYADENOSINE. JRNL REF BIOCHEMISTRY V. 36 11069 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9333324 JRNL DOI 10.1021/BI971306U 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, REMARK 3 FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR REMARK 3 DYNAMICS/ENERGY MINIMIZATION CALCULATIONS: (1) REMARK 3 INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM REMARK 3 RELAXATION MATRIX ANALYSIS OF NOE DATA; (2) IMINO PROTON REMARK 3 HYDROGEN BOND RESTRAINTS FOR ALL BASE PAIRS EXCEPT THE REMARK 3 CENTRAL DA-DG MISMATCH PAIR. THE MODIFIED DA RESIDUE OF REMARK 3 THIS MINOR CONFORMER DISPLAYED A C2'-ENDO SUGAR PUCKER AND REMARK 3 AN ANTI GLYCOSIDIC BOND. IT FORMED AN ANTI:ANTI BASE PAIR REMARK 3 CONTAINING TWO HYDROGEN BONDS WITH THE OPPOSITE DG. THE REMARK 3 MODIFIED DA RESIDUE OF THE MAJOR CONFORMER OF THIS REMARK 3 MOLECULE [YEH ET AL. (1995) BIOCHEMISTRY 34, 13570-13581] REMARK 3 DISPLAYED C3'-ENDO SUGAR PUCKER AND A SYN GLYCOSIDIC BOND. REMARK 3 THE MAJOR CONFORMER MODIFIED DA RESIDUE FORMED A SYN:ANTI REMARK 3 BASE PAIR CONTAINING NON-WATSON CRICK HYDROGEN BONDS WITH REMARK 3 THE OPPOSITE DG. REMARK 3 MORE REFINEMENT DETAILS CAN BE FOUND IN THE PRIMARY JOURNAL REMARK 3 CITATION (SCHWARTZ ET AL.,1997). REMARK 4 REMARK 4 1BPS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008021. 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; 2D EXCHANGE REMARK 210 -ONLY SPECTRA REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS 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 OF REMARK 210 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 : 1 REMARK 210 REMARK 210 REMARK: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED REMARK 210 USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY EXPERIMENTS DONE REMARK 210 IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D ROESY, TOCSY, AND REMARK 210 EXCHANGE-ONLY EXPERIMENTS WERE USED IN THE CHEMICAL SHIFT REMARK 210 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 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 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. = -4.8 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