HEADER DNA 11-JAN-01 1HX4 TITLE MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS DETERMINES DNA TITLE 2 ADDUCT CONFORMATION: A LINK TO TUMORIGENIC ACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED FROM ABI-DNA SYNTHESIZER; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHESIZED FROM ABI-DNA SYNTHESIZER KEYWDS 1R-TRANS-ANTI-BPH-N2-G ADDUCT, CARCINOGEN-DNA ADDUCT, KEYWDS 2 BENZO[C]PHENANTHRENE DNA ADDUCT, DNA EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR D.J.PATEL,C.H.LIN,N.E.GEACINTOV,S.BROYDE,X.HUANG,A.KOLBANOVSKII, AUTHOR 2 B.E.HINGERTY,S.AMIN REVDAT 4 22-MAY-24 1HX4 1 REMARK REVDAT 3 23-FEB-22 1HX4 1 REMARK LINK REVDAT 2 24-FEB-09 1HX4 1 VERSN REVDAT 1 21-MAR-01 1HX4 0 JRNL AUTH C.H.LIN,X.HUANG,A.KOLBANOVSKII,B.E.HINGERTY,S.AMIN,S.BROYDE, JRNL AUTH 2 N.E.GEACINTOV,D.J.PATEL JRNL TITL MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS JRNL TITL 2 DETERMINES DNA ADDUCT CONFORMATION: A LINK TO TUMORIGENIC JRNL TITL 3 ACTIVITY. JRNL REF J.MOL.BIOL. V. 306 1059 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11237618 JRNL DOI 10.1006/JMBI.2001.4425 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, X-PLOR 3.1 REMARK 3 AUTHORS : VARIAN ASSOCIATES INC. (VNMR), BRUNGER, A. T. (X REMARK 3 -PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NONEXCHANGEABLE INTERPROTON DISTANCE REMARK 3 RESTRAINTS WERE OBTAINED FROM THE BUILDUP OF NOE CROSS PEAK REMARK 3 VOLUMES IN NOESY DATA SETS (55, 100, 150 AND 200 MS MIXING TIMES) REMARK 3 ON THE 1S-(-)-TRANS-ANTI-(BPH)G*C AND THE 1R-(+)-TRANS-ANTI- REMARK 3 (BPH)G*C 11-MER DNA DUPLEX ADDUCTS IN D2O BUFFER AT 23 AND 18 SC, REMARK 3 RESPECTIVELY, AND BOUNDS WERE SET BETWEEN 15% AND 25% OF THE REMARK 3 CALCULATED DISTANCES USING THE FIXED CYTIDINE H5-H6 REFERENCE REMARK 3 DISTANCE OF 2.45 . NON-STEREOSPECIFIC ASSIGNMENTS WERE TREATED REMARK 3 WITH R-6 AVERAGING. INTERPROTON DISTANCE RESTRAINTS INVOLVING REMARK 3 EXCHANGEABLE PROTONS OF THE SAME COMPLEX WERE OBTAINED FROM REMARK 3 NOESY SPECTRA (90 AND 150 MS MIXING TIMES) IN H2O BUFFER AT 4 SC REMARK 3 WITH BOUNDS SET BETWEEN 20% AND 25% OF THE CALCULATED DISTANCE REMARK 3 USING THE THYMINE IMINO TO ADENINE H2 REFERENCE DISTANCE OF 2.91 REMARK 3 ACROSS AN A*T BASE PAIR. REMARK 4 REMARK 4 1HX4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000012648. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1R-TRANS-ANTI-BPH (CARCINOGEN) REMARK 210 COVALENTLY BOUND TO 11MER DNA REMARK 210 DUPLEX REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; P-COSY; 1H-31P HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX FELIX2000 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, RELAXATION REMARK 210 MATRIX REFINEMENTS, ENERGE REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 9 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: D2O NMR EXPERIMENTS WERE PERFORMED AT 13 DEGREE C, H2O NMR REMARK 210 EXPERIMENTS WERE PERFORMED AT 4 DEGREE C 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 DC A 2 N1 DC A 2 C6 -0.038 REMARK 500 1 DG A 6 N7 DG A 6 C8 0.045 REMARK 500 1 DA A 9 C3' DA A 9 C2' -0.059 REMARK 500 1 DG B 12 N7 DG B 12 C8 0.041 REMARK 500 1 DG B 13 N7 DG B 13 C8 0.050 REMARK 500 1 DA B 15 N7 DA B 15 C8 0.043 REMARK 500 1 DG B 16 N7 DG B 16 C8 0.045 REMARK 500 1 DG B 18 N7 DG B 18 C8 0.040 REMARK 500 1 DG B 21 N7 DG B 21 C8 0.045 REMARK 500 1 DG B 22 N7 DG B 22 C8 0.045 REMARK 500 2 DC A 2 N1 DC A 2 C6 -0.037 REMARK 500 2 DG A 6 N7 DG A 6 C8 0.046 REMARK 500 2 DT A 8 C6 DT A 8 N1 -0.043 REMARK 500 2 DA A 9 C3' DA A 9 C2' -0.057 REMARK 500 2 DG B 12 N7 DG B 12 C8 0.046 REMARK 500 2 DG B 13 C3' DG B 13 C2' -0.049 REMARK 500 2 DG B 13 N7 DG B 13 C8 0.046 REMARK 500 2 DT B 14 C6 DT B 14 N1 -0.043 REMARK 500 2 DG B 16 N7 DG B 16 C8 0.043 REMARK 500 2 DG B 18 N7 DG B 18 C8 0.043 REMARK 500 2 DG B 21 N7 DG B 21 C8 0.048 REMARK 500 2 DG B 22 N7 DG B 22 C8 0.046 REMARK 500 3 DC A 2 N1 DC A 2 C6 -0.038 REMARK 500 3 DG A 6 N7 DG A 6 C8 0.047 REMARK 500 3 DT A 8 C6 DT A 8 N1 -0.042 REMARK 500 3 DA A 9 C3' DA A 9 C2' -0.059 REMARK 500 3 DG B 12 N7 DG B 12 C8 0.047 REMARK 500 3 DG B 13 N7 DG B 13 C8 0.049 REMARK 500 3 DT B 14 C6 DT B 14 N1 -0.043 REMARK 500 3 DG B 16 N7 DG B 16 C8 0.042 REMARK 500 3 DG B 18 N7 DG B 18 C8 0.042 REMARK 500 3 DG B 21 N7 DG B 21 C8 0.048 REMARK 500 3 DG B 22 N7 DG B 22 C8 0.042 REMARK 500 4 DC A 2 N1 DC A 2 C6 -0.039 REMARK 500 4 DG A 6 N7 DG A 6 C8 0.048 REMARK 500 4 DA A 9 C3' DA A 9 C2' -0.057 REMARK 500 4 DG B 12 N7 DG B 12 C8 0.048 REMARK 500 4 DG B 13 N7 DG B 13 C8 0.051 REMARK 500 4 DT B 14 C6 DT B 14 N1 -0.043 REMARK 500 4 DG B 16 N7 DG B 16 C8 0.042 REMARK 500 4 DG B 18 N7 DG B 18 C8 0.041 REMARK 500 4 DG B 21 N7 DG B 21 C8 0.046 REMARK 500 4 DG B 22 N7 DG B 22 C8 0.045 REMARK 500 5 DC A 2 N1 DC A 2 C6 -0.038 REMARK 500 5 DG A 6 N7 DG A 6 C8 0.047 REMARK 500 5 DA A 9 C3' DA A 9 C2' -0.059 REMARK 500 5 DG B 12 N7 DG B 12 C8 0.044 REMARK 500 5 DG B 13 C3' DG B 13 C2' -0.064 REMARK 500 5 DG B 13 N7 DG B 13 C8 0.049 REMARK 500 5 DG B 16 N7 DG B 16 C8 0.041 REMARK 500 REMARK 500 THIS ENTRY HAS 95 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 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DC A 5 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DC A 5 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 6 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC A 7 N1 - C1' - C2' ANGL. DEV. = 9.9 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 8 C4 - C5 - C7 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DT A 8 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DC A 10 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 11 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG B 12 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG B 13 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG B 13 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DT B 14 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT B 14 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT B 14 C6 - C5 - C7 ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DT B 14 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 1 DG B 16 C1' - O4' - C4' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC B 17 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC B 17 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC B 17 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DG B 18 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DT B 20 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT B 20 C4 - C5 - C7 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT B 20 C6 - C5 - C7 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DG B 21 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 2 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DT A 4 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 2 DT A 4 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DG A 6 C1' - O4' - C4' ANGL. DEV. = -8.5 DEGREES REMARK 500 2 DG A 6 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DC A 7 N1 - C1' - C2' ANGL. DEV. = 9.7 DEGREES REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT A 8 C4 - C5 - C7 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -7.5 DEGREES REMARK 500 2 DT A 8 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 314 ANGLE DEVIATIONS. 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 BPJ A 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HWV RELATED DB: PDB REMARK 900 1S-TRANS-ANTI-(BPH)-N2-DG ADDUCT, CARCINOGEN-DNA ADDUCT DBREF 1HX4 A 1 11 PDB 1HX4 1HX4 1 11 DBREF 1HX4 B 12 22 PDB 1HX4 1HX4 12 22 SEQRES 1 A 11 DC DC DA DT DC DG DC DT DA DC DC SEQRES 1 B 11 DG DG DT DA DG DC DG DA DT DG DG HET BPJ A 25 36 HETNAM BPJ (1R)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4- HETNAM 2 BPJ TRIOL HETSYN BPJ 1R-TRANS-ANTI-BENZO[C]PHENANTHRENE FORMUL 3 BPJ C18 H16 O3 LINK N2 DG A 6 C1 BPJ A 25 1555 1555 1.34 SITE 1 AC1 6 DG A 6 DC A 7 DG B 16 DC B 17 SITE 2 AC1 6 DG B 18 DA 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 MODEL 1