HEADER DNA 03-OCT-00 1FYY TITLE HPRT GENE MUTATION HOTSPOT WITH A BPDE2(10R) ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HPRT DNA WITH BENZO[A]PYRENE-ADDUCTED DA7; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*TP*GP*CP*CP*CP*TP*TP*GP*AP*CP*TP*A)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE CONTAINS A MUTATIONAL HOTSPOT SOURCE 4 IN THE MOUSE HPRT GENE WITH A CHEMICALLY SYNTHESIZED SOURCE 5 BENZO[A]PYRENE ADDUCT; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES KEYWDS DNA LESIONS, BENZO[A]PYRENE, HPRT GENE, DIOL EPOXIDE KEYWDS 2 ADDUCTS, SYN-ANTI INTERCONVERSION EXPDTA SOLUTION NMR AUTHOR D.E.VOLK,J.S.RICE,B.A.LUXON,H.J.C.YEH,C.LIANG,G.XIE, AUTHOR 2 J.M.SAYER,D.M.JERINA,D.G.GORENSTEIN REVDAT 3 24-FEB-09 1FYY 1 VERSN REVDAT 2 01-APR-03 1FYY 1 JRNL REVDAT 1 06-DEC-00 1FYY 0 JRNL AUTH D.E.VOLK,J.S.RICE,B.A.LUXON,H.J.YEH,C.LIANG,G.XIE, JRNL AUTH 2 J.M.SAYER,D.M.JERINA,D.G.GORENSTEIN JRNL TITL NMR EVIDENCE FOR SYN-ANTI INTERCONVERSION OF A JRNL TITL 2 TRANS OPENED (10R)-DA ADDUCT OF BENZO[A]PYRENE JRNL TITL 3 (7S,8R)-DIOL (9R,10S)-EPOXIDE IN A DNA DUPLEX. JRNL REF BIOCHEMISTRY V. 39 14040 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11087351 JRNL DOI 10.1021/BI001669L REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5 REMARK 3 AUTHORS : CASE, D. A. ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FYY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-00. REMARK 100 THE RCSB ID CODE IS RCSB012031. 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 : 100 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DUPLEX, 20 MM PHOSPHATE REMARK 210 BUFFER, 56 MM NACL, PH 6.8-7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MORASS 2.5 REMARK 210 METHOD USED : MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : SUBMITTED THE AVERAGE REMARK 210 STRUCTURE OF THE 10 STRUCTURES REMARK 210 DETERMINED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 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 DA A 6 C5' DA A 6 C4' 0.047 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 DT A 1 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT A 1 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA A 2 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DC A 5 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 DA A 7 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 9 N1 - C6 - O6 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 12 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT B 13 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC B 15 O4' - C4' - C3' ANGL. DEV. = 6.1 DEGREES REMARK 500 DC B 16 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT B 19 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 21 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 22 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT B 23 O4' - C4' - C3' ANGL. DEV. = 6.3 DEGREES REMARK 500 DA B 24 N1 - C6 - N6 ANGL. DEV. = -4.3 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 5 0.12 SIDE_CHAIN REMARK 500 DA A 6 0.08 SIDE_CHAIN REMARK 500 DA A 7 0.12 SIDE_CHAIN REMARK 500 DG A 9 0.08 SIDE_CHAIN REMARK 500 DC A 11 0.08 SIDE_CHAIN REMARK 500 DG B 14 0.07 SIDE_CHAIN REMARK 500 DT B 19 0.16 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 25 DBREF 1FYY A 1 12 PDB 1FYY 1FYY 1 12 DBREF 1FYY B 13 24 PDB 1FYY 1FYY 13 24 SEQRES 1 A 12 DT DA DG DT DC DA DA DG DG DG DC DA SEQRES 1 B 12 DT DG DC DC DC DT DT DG DA DC DT DA HET BAP A 25 38 HETNAM BAP 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE FORMUL 3 BAP C20 H16 O3 LINK N6 DA A 7 C4' BAP A 25 1555 1555 1.49 SITE 1 AC1 5 DC A 5 DA A 6 DA A 7 DT B 18 SITE 2 AC1 5 DT B 19 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 141 0 1 0 0 0 2 6 0 0 0 2 END