HEADER DNA 22-MAY-07 2Z2G TITLE NMR STRUCTURE OF THE IQ-MODIFIED DODECAMER CTC[IQ]GGCGCCATC COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*DCP*DTP*DCP*DGP*DGP*DCP*DGP*DCP*DCP*DAP*DTP*DC)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*DGP*DAP*DTP*DGP*DGP*DCP*DGP*DCP*DCP*DGP*DAP*DG)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE UNMODIFIED OLIGODEOXYNUCLEOTIDE 5'- SOURCE 4 D(GATGGCGCCGAG)-3' WAS OBTAINED FROM THE MIDLAND CERTIFIED SOURCE 5 REAGENT COMPANY, AND HAD BEEN PURIFIED BY ANION EXCHANGE SOURCE 6 CHROMATOGRAPHY. THE IQ-ADDUCTED OLIGODEOXYNUCLEOTIDES 5'- SOURCE 7 D(CTCXGCGCCATC)-3' AND 5'-D(CTCGXCGCCATC)-3' WERE SOURCE 8 SYNTHESIZED AND PURIFIED AS DESCRIBED IN PAPER BY ELMQUIST, SOURCE 9 C. ERIC.[J. AM. CHEM. SOC., VOL. 126, NO. 36, 2004].; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES KEYWDS NMR STRUCTURE, NAR1IQ1, RMD CALCULATIONS, NOESY, COSY, KEYWDS 2 REFINEMENT, IQ, ADDUCT, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR F.WANG,C.E.ELMQUIST,J.S.STOVER,C.J.RIZZO,M.P.STONE REVDAT 2 24-FEB-09 2Z2G 1 VERSN REVDAT 1 02-OCT-07 2Z2G 0 JRNL AUTH F.WANG,C.E.ELMQUIST,J.S.STOVER,C.J.RIZZO,M.P.STONE JRNL TITL DNA SEQUENCE MODULATES THE CONFORMATION OF THE JRNL TITL 2 FOOD MUTAGEN JRNL TITL 3 2-AMINO-3-METHYLIMIDAZO[4,5-F]QUINOLINE IN THE JRNL TITL 4 RECOGNITION SEQUENCE OF THE NARI RESTRICTION ENZYME JRNL REF BIOCHEMISTRY V. 46 8498 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17602664 JRNL DOI 10.1021/BI700361U REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z2G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAY-07. REMARK 100 THE RCSB ID CODE IS RCSB027436. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 288; 298 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 0.1M NACL; 0.1M NACL; 0.1M REMARK 210 NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7MM MODIFIED DUPLEX, 10MM REMARK 210 PHOSPHATE BUFFER WITH 0.1M REMARK 210 NACL AND 0.05MM NA2EDTA (PH REMARK 210 7.0), D2O; 0.7MM MODIFIED REMARK 210 DUPLEX, 10MM PHOSPHATE BUFFER REMARK 210 WITH 0.1M NACL AND 0.05MM REMARK 210 NA2EDTA (PH 7.0), 90% H2O AND REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, MAGNITUDE COSY, E- REMARK 210 COSY, DQF-COSY, P-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : TXI, QXI REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95.0, MARDIGRAS 5.2, REMARK 210 CORMA 5.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 12 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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 1 DC A 1 C4' DC A 1 C3' -0.072 REMARK 500 1 DC A 3 N1 DC A 3 C6 -0.045 REMARK 500 1 DG A 5 N7 DG A 5 C8 -0.039 REMARK 500 1 DA A 10 C3' DA A 10 C2' -0.051 REMARK 500 1 DA A 10 C8 DA A 10 N9 -0.053 REMARK 500 1 DT A 11 C5 DT A 11 C6 -0.065 REMARK 500 1 DG B 13 C8 DG B 13 N9 -0.045 REMARK 500 1 DA B 14 C8 DA B 14 N9 -0.072 REMARK 500 1 DG B 17 C8 DG B 17 N9 -0.065 REMARK 500 1 DC B 20 C3' DC B 20 C2' -0.063 REMARK 500 1 DC B 20 N1 DC B 20 C6 -0.038 REMARK 500 1 DG B 22 C8 DG B 22 N9 -0.042 REMARK 500 1 DG B 24 C8 DG B 24 N9 -0.052 REMARK 500 2 DC A 1 C4' DC A 1 C3' -0.073 REMARK 500 2 DC A 3 N1 DC A 3 C6 -0.045 REMARK 500 2 DG A 5 N7 DG A 5 C8 -0.040 REMARK 500 2 DA A 10 C3' DA A 10 C2' -0.051 REMARK 500 2 DA A 10 C8 DA A 10 N9 -0.054 REMARK 500 2 DT A 11 C5 DT A 11 C6 -0.065 REMARK 500 2 DG B 13 C8 DG B 13 N9 -0.046 REMARK 500 2 DA B 14 C8 DA B 14 N9 -0.071 REMARK 500 2 DG B 17 C8 DG B 17 N9 -0.066 REMARK 500 2 DC B 20 C3' DC B 20 C2' -0.063 REMARK 500 2 DC B 20 N1 DC B 20 C6 -0.037 REMARK 500 2 DG B 22 C8 DG B 22 N9 -0.043 REMARK 500 2 DG B 24 C8 DG B 24 N9 -0.053 REMARK 500 3 DC A 1 C4' DC A 1 C3' -0.073 REMARK 500 3 DC A 3 N1 DC A 3 C6 -0.045 REMARK 500 3 DG A 5 N7 DG A 5 C8 -0.040 REMARK 500 3 DA A 10 C3' DA A 10 C2' -0.050 REMARK 500 3 DA A 10 C8 DA A 10 N9 -0.052 REMARK 500 3 DT A 11 C5 DT A 11 C6 -0.065 REMARK 500 3 DG B 13 C8 DG B 13 N9 -0.045 REMARK 500 3 DA B 14 C8 DA B 14 N9 -0.071 REMARK 500 3 DG B 17 C8 DG B 17 N9 -0.066 REMARK 500 3 DC B 20 C3' DC B 20 C2' -0.061 REMARK 500 3 DC B 20 N1 DC B 20 C6 -0.038 REMARK 500 3 DG B 22 C8 DG B 22 N9 -0.043 REMARK 500 3 DG B 24 C8 DG B 24 N9 -0.053 REMARK 500 4 DC A 1 C4' DC A 1 C3' -0.073 REMARK 500 4 DC A 3 N1 DC A 3 C6 -0.044 REMARK 500 4 DG A 5 N7 DG A 5 C8 -0.041 REMARK 500 4 DA A 10 C3' DA A 10 C2' -0.052 REMARK 500 4 DA A 10 C8 DA A 10 N9 -0.052 REMARK 500 4 DT A 11 C5 DT A 11 C6 -0.065 REMARK 500 4 DG B 13 C8 DG B 13 N9 -0.046 REMARK 500 4 DA B 14 C8 DA B 14 N9 -0.071 REMARK 500 4 DG B 17 C8 DG B 17 N9 -0.065 REMARK 500 4 DC B 20 C3' DC B 20 C2' -0.062 REMARK 500 4 DC B 20 N1 DC B 20 C6 -0.037 REMARK 500 REMARK 500 THIS ENTRY HAS 129 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 1 C5' - C4' - C3' ANGL. DEV. = -12.1 DEGREES REMARK 500 1 DC A 1 C6 - N1 - C2 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 1 C6 - N1 - C1' ANGL. DEV. = -7.4 DEGREES REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 3 C6 - N1 - C2 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA A 10 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 11 C4 - C5 - C6 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 11 C4 - C5 - C7 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DT A 11 C6 - C5 - C7 ANGL. DEV. = -9.8 DEGREES REMARK 500 1 DC A 12 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 13 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG B 13 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DA B 14 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 14 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA B 14 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DT B 15 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 15 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG B 16 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 16 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG B 17 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG B 17 N7 - C8 - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG B 19 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC B 21 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG B 22 N7 - C8 - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DA B 23 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DG B 24 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG B 24 N7 - C8 - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 DC A 1 C5' - C4' - C3' ANGL. DEV. = -12.0 DEGREES REMARK 500 2 DC A 1 C6 - N1 - C2 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC A 1 C6 - N1 - C1' ANGL. DEV. = -7.5 DEGREES REMARK 500 2 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 406 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HKB RELATED DB: NDB REMARK 900 UNMODIFIED DUPLEX REMARK 900 RELATED ID: 2HKC RELATED DB: NDB REMARK 900 CTCGGC[IQ]GCCATC DBREF 2Z2G A 1 12 PDB 2Z2G 2Z2G 1 12 DBREF 2Z2G B 13 24 PDB 2Z2G 2Z2G 13 24 SEQRES 1 A 12 DC DT DC DG DG DC DG DC DC DA DT DC SEQRES 1 B 12 DG DA DT DG DG DC DG DC DC DG DA DG HET GIQ A 25 24 HETNAM GIQ 3-METHYL-3H-IMIDAZO[4,5-F]QUINOLIN-2-AMINE HETSYN GIQ 2-AMINO-3-METHYLIMIDAZO[4,5-F]QUINOLINE FORMUL 3 GIQ C11 H10 N4 LINK C8 DG A 4 N10 GIQ A 25 1555 1555 1.41 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 MASTER 204 0 1 0 0 0 0 6 0 0 0 2 END