HEADER DNA 09-JUL-03 1PYJ TITLE SOLUTION STRUCTURE OF AN O6-[4-OXO-4-(3-PYRIDYL)BUTYL]GUANINE ADDUCT TITLE 2 IN AN 11MER DNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*TP*AP*TP*GP*GP*CP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D*GP*GP*GP*CP*CP*AP*TP*AP*TP*GP*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 DNA ADDUCT, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR L.A.PETERSON,C.VU,B.E.HINGERTY,S.BROYDE,M.COSMAN REVDAT 4 01-MAY-24 1PYJ 1 REMARK LINK REVDAT 3 06-AUG-14 1PYJ 1 ATOM HETATM HETNAM LINK REVDAT 3 2 1 REMARK SEQRES VERSN REVDAT 2 24-FEB-09 1PYJ 1 VERSN REVDAT 1 20-APR-04 1PYJ 0 JRNL AUTH L.A.PETERSON,C.VU,B.E.HINGERTY,S.BROYDE,M.COSMAN JRNL TITL SOLUTION STRUCTURE OF AN JRNL TITL 2 O6-[4-OXO-4-(3-PYRIDYL)BUTYL]GUANINE ADDUCT IN AN 11 MER DNA JRNL TITL 3 DUPLEX: EVIDENCE FOR FORMATION OF A BASE TRIPLEX. JRNL REF BIOCHEMISTRY V. 42 13134 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 14609323 JRNL DOI 10.1021/BI035217V REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, DUPLEX REMARK 3 AUTHORS : VARIAN (VNMR), HINGERTY AND BROYDE (DUPLEX) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 325 RESTRAINTS (271 DNA-DNA, 22 POB-DNA, 5 POB-POB, 29 H-BONDS). REMARK 4 REMARK 4 1PYJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019700. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.00 REMARK 210 IONIC STRENGTH : 0.1 M NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [POB]DG-DC 11MER DUPLEX REMARK 210 ADDUCT IN 600 UL 10 MM SODIUM REMARK 210 PHOSPHATE, 0.1 M NACL, 0.1 MM REMARK 210 EDTA, PH7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY 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 : FELIX 97, DUPLEX REMARK 210 METHOD USED : MOLECULAR MECHANICS IN TORSION REMARK 210 ANGLE SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL 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: 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 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 DG A 8 C8 DG A 8 N9 -0.045 REMARK 500 DG B 12 C8 DG B 12 N9 -0.043 REMARK 500 DG B 13 C8 DG B 13 N9 -0.044 REMARK 500 DG B 14 C8 DG B 14 N9 -0.045 REMARK 500 DG B 21 C8 DG B 21 N9 -0.043 REMARK 500 DG B 22 C8 DG B 22 N9 -0.044 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 DC A 2 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DA A 3 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DT A 4 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DA A 5 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DT A 6 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG A 8 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DG A 8 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG A 8 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC A 9 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DC A 10 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DC A 11 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG B 12 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 12 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 12 N7 - C8 - N9 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG B 13 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG B 13 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 13 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 13 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 14 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG B 14 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 14 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 14 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC B 15 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DC B 16 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DA B 17 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DT B 18 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DA B 19 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DT B 20 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DG B 21 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DG B 21 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 21 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 21 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 22 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG B 22 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 22 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1PYJ A 1 11 PDB 1PYJ 1PYJ 1 11 DBREF 1PYJ B 12 22 PDB 1PYJ 1PYJ 12 22 SEQRES 1 A 11 DC DC DA DT DA DT XPB DG DC DC DC SEQRES 1 B 11 DG DG DG DC DC DA DT DA DT DG DG MODRES 1PYJ XPB A 7 DG HET XPB A 7 53 HETNAM XPB O6-[4-OXO-4-(3-PYRIDYL)BUTYL]-2'-DEOXYGUANOSINE-5'- HETNAM 2 XPB MONOPHOSPHATE FORMUL 1 XPB C19 H23 N6 O8 P LINK O3' DT A 6 P XPB A 7 1555 1555 1.60 LINK O3' XPB A 7 P DG A 8 1555 1555 1.60 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