HEADER DNA 05-FEB-04 1S9O TITLE SOLUTION STRUCTURE OF THE NITROUS ACID INDUCED DNA INTERSTRAND CROSS- TITLE 2 LINKED DODECAMER DUPLEX CGCTAC(G)TAGCG WITH THE CROSS-LINKED GUANINES TITLE 3 DENOTED (G) CAVEAT 1S9O RESIDUE DG B7 HAS EXTRA HYDROGEN ATOM H6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*TP*AP*CP*GP*TP*AP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICAL SYNTHESIS DESCRIBED IN HARWOOD ET AL. (1999) SOURCE 4 J. AM. CHEM. SOC. 121, 5081-5082 KEYWDS DNA, NITROUS ACID, CROSS-LINK, EXTRAHELICAL CYTOSINES, MINOR GROOVE EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR N.B.EDFELDT,E.A.HARWOOD,S.T.SIGURDSSON,P.B.HOPKINS,B.R.REID REVDAT 3 26-MAY-10 1S9O 1 HET REVDAT 2 24-FEB-09 1S9O 1 VERSN REVDAT 1 01-NOV-05 1S9O 0 JRNL AUTH N.B.EDFELDT,E.A.HARWOOD,S.T.SIGURDSSON,P.B.HOPKINS,B.R.REID JRNL TITL SOLUTION STRUCTURE OF A NITROUS ACID INDUCED DNA JRNL TITL 2 INTERSTRAND CROSS-LINK. JRNL REF NUCLEIC ACIDS RES. V. 32 2785 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 15155847 JRNL DOI 10.1093/NAR/GKH606 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 1 REMARK 3 AUTHORS : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 647 DISTANCE RESTRAINTS (514 ARE NOE-DERIVED, 42 FROM HYDROGEN REMARK 3 BONDING, 81 REPULSIVE) AND 176 DIHEDRAL ANGLE RESTRAINTS (104 REMARK 3 BACKBONE, 72 CHIRAL). REMARK 4 REMARK 4 1S9O COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-04. REMARK 100 THE RCSB ID CODE IS RCSB021541. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 200MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM DNA, 10MM PHOSPHATE PH 7.0, REMARK 210 200MM NACL, 1MM EDTA; 1MM DNA, REMARK 210 10MM PHOSPHATE PH 7.0, 200MM REMARK 210 NACL, 1MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 1H-31P HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 1, FELIX 1, DGII 1, REMARK 210 DISCOVER 1, BIRDER 97 REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR REMARK 210 DYNAMICS, MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 N2 ATOM OF G7 IS MISSING IN ALL MODELS DUE TO NITROUS ACID REMARK 400 INDUCED DNA INTERSTRAND CROSS-LINKED DODECAMER DUPLEX REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-12 REMARK 470 RES CSSEQI ATOMS REMARK 470 DG A 7 N2 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 C2 DG A 7 N2 DG B 7 1.35 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 DG B 7 C6 DG B 7 O6 0.127 REMARK 500 2 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 3 DG B 7 C6 DG B 7 O6 0.127 REMARK 500 4 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 5 DG B 7 C6 DG B 7 O6 0.126 REMARK 500 6 DG B 7 C6 DG B 7 O6 0.126 REMARK 500 7 DG A 7 C6 DG A 7 O6 0.126 REMARK 500 8 DG A 7 C6 DG A 7 O6 0.127 REMARK 500 9 DG A 7 C6 DG A 7 O6 0.127 REMARK 500 10 DG A 7 C6 DG A 7 O6 0.126 REMARK 500 11 DG A 7 C6 DG A 7 O6 0.126 REMARK 500 12 DG A 7 C6 DG A 7 O6 0.125 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA B 5 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 7 C5 - C6 - O6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA B 5 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG B 7 C5 - C6 - O6 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DA B 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DG B 7 C5 - C6 - O6 ANGL. DEV. = -5.5 DEGREES REMARK 500 3 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DC B 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 4 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 186 ANGLE DEVIATIONS. 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 1 DG A 2 0.06 SIDE CHAIN REMARK 500 1 DC A 6 0.07 SIDE CHAIN REMARK 500 1 DG A 12 0.07 SIDE CHAIN REMARK 500 1 DG B 2 0.07 SIDE CHAIN REMARK 500 1 DC B 6 0.07 SIDE CHAIN REMARK 500 1 DG B 12 0.07 SIDE CHAIN REMARK 500 2 DG A 2 0.06 SIDE CHAIN REMARK 500 2 DC A 6 0.07 SIDE CHAIN REMARK 500 2 DG A 12 0.07 SIDE CHAIN REMARK 500 2 DG B 2 0.07 SIDE CHAIN REMARK 500 2 DC B 6 0.07 SIDE CHAIN REMARK 500 2 DG B 12 0.07 SIDE CHAIN REMARK 500 3 DG A 2 0.06 SIDE CHAIN REMARK 500 3 DC A 6 0.07 SIDE CHAIN REMARK 500 3 DG A 12 0.07 SIDE CHAIN REMARK 500 3 DG B 2 0.07 SIDE CHAIN REMARK 500 3 DC B 6 0.07 SIDE CHAIN REMARK 500 3 DG B 12 0.07 SIDE CHAIN REMARK 500 4 DG A 2 0.07 SIDE CHAIN REMARK 500 4 DC A 6 0.07 SIDE CHAIN REMARK 500 4 DG A 12 0.08 SIDE CHAIN REMARK 500 4 DG B 2 0.07 SIDE CHAIN REMARK 500 4 DA B 9 0.05 SIDE CHAIN REMARK 500 4 DG B 12 0.07 SIDE CHAIN REMARK 500 5 DC A 6 0.07 SIDE CHAIN REMARK 500 5 DG A 12 0.07 SIDE CHAIN REMARK 500 5 DG B 2 0.07 SIDE CHAIN REMARK 500 5 DC B 6 0.07 SIDE CHAIN REMARK 500 5 DG B 12 0.07 SIDE CHAIN REMARK 500 6 DG A 2 0.06 SIDE CHAIN REMARK 500 6 DC A 6 0.07 SIDE CHAIN REMARK 500 6 DG A 12 0.07 SIDE CHAIN REMARK 500 6 DG B 2 0.06 SIDE CHAIN REMARK 500 6 DC B 6 0.07 SIDE CHAIN REMARK 500 6 DG B 12 0.07 SIDE CHAIN REMARK 500 7 DG A 2 0.06 SIDE CHAIN REMARK 500 7 DC A 6 0.07 SIDE CHAIN REMARK 500 7 DG A 12 0.07 SIDE CHAIN REMARK 500 7 DG B 2 0.06 SIDE CHAIN REMARK 500 7 DC B 6 0.07 SIDE CHAIN REMARK 500 7 DG B 12 0.07 SIDE CHAIN REMARK 500 8 DG A 2 0.06 SIDE CHAIN REMARK 500 8 DC A 6 0.07 SIDE CHAIN REMARK 500 8 DG A 12 0.07 SIDE CHAIN REMARK 500 8 DG B 2 0.06 SIDE CHAIN REMARK 500 8 DC B 6 0.07 SIDE CHAIN REMARK 500 8 DG B 12 0.07 SIDE CHAIN REMARK 500 9 DG A 2 0.07 SIDE CHAIN REMARK 500 9 DC A 6 0.07 SIDE CHAIN REMARK 500 9 DG A 12 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 68 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S9N RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE NITROUS ACID INDUCED DNA REMARK 900 INTERSTRAND CROSS-LINKED DODECAMER DUPLEX GCATCC(G)GATGC REMARK 900 WITH THE CROSS-LINKED GUANINES DENOTED (G) DBREF 1S9O A 1 12 PDB 1S9O 1S9O 1 12 DBREF 1S9O B 1 12 PDB 1S9O 1S9O 1 12 SEQRES 1 A 12 DC DG DC DT DA DC DG DT DA DG DC DG SEQRES 1 B 12 DC DG DC DT DA DC DG DT DA DG DC DG 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 249 0 0 0 0 0 0 6 0 0 0 2 END