HEADER DNA 03-JUL-06 2HKC TITLE NMR STRUCTURE OF THE IQ-MODIFIED DODECAMER CTCGGC[IQ]GCCATC COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: THE UNMODIFIED OLIGODEOXYNUCLEOTIDES 5'- SOURCE 6 D(CTCGGCGCCATC)-3' AND 5'-D(GATGGCGCCGAG)-3' WERE OBTAINED FROM THE SOURCE 7 MIDLAND CERTIFIED REAGENT COMPANY, AND HAD BEEN PURIFIED BY ANION SOURCE 8 EXCHANGE CHROMATOGRAPHY. THE IQ-ADDUCTED OLIGODEOXYNUCLEOTIDE 5'- SOURCE 9 D(CTCGGCXCCATC)-3' WAS SYNTHESIZED AND PURIFIED AS DESCRIBED IN SOURCE 10 PAPER BY ELMQUIST, C. ERIC [J. AM. CHEM. SOC., VOL. 126, NO. 36, SOURCE 11 2004].; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS NAR1IQ3, RMD CALCULATIONS, ANNEAL, NOESY, COSY, REFINEMENT, IQ, KEYWDS 2 ADDUCT, HCA, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR F.WANG,N.E.DEMURO,C.E.ELMQUIST,J.S.STOVER,C.J.RIZZO,M.P.STONE REVDAT 4 29-MAY-24 2HKC 1 REMARK REVDAT 3 03-NOV-21 2HKC 1 SOURCE REMARK LINK REVDAT 2 24-FEB-09 2HKC 1 VERSN REVDAT 1 03-OCT-06 2HKC 0 JRNL AUTH F.WANG,N.E.DEMURO,C.E.ELMQUIST,J.S.STOVER,C.J.RIZZO, JRNL AUTH 2 M.P.STONE JRNL TITL BASE-DISPLACED INTERCALATED STRUCTURE OF THE FOOD MUTAGEN JRNL TITL 2 2-AMINO-3-METHYLIMIDAZO[4,5-F]QUINOLINE IN THE RECOGNITION JRNL TITL 3 SEQUENCE OF THE NARI RESTRICTION ENZYME, A HOTSPOT FOR -2 BP JRNL TITL 4 DELETIONS. JRNL REF J.AM.CHEM.SOC. V. 128 10085 2006 JRNL REFN ISSN 0002-7863 JRNL PMID 16881637 JRNL DOI 10.1021/JA062004V 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 2HKC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038444. 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 : 0.1 M NACL; 0.1 M NACL; 0.1 M REMARK 210 NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM MODIFIED DUPLEX, 10 MM REMARK 210 PHOSPHATE BUFFER, 0.1 M NACL, REMARK 210 0.05 MM NA2EDTA, 100% D2O; 0.7 REMARK 210 MM MODIFIED DUPLEX, 10 MM REMARK 210 PHOSPHATE BUFFER, 0.1 M NACL, REMARK 210 0.05 MM NA2EDTA, 90% H2O/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 : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95.0, MARDIGRAS 5.2, CORMA REMARK 210 5.2 REMARK 210 METHOD USED : SIMULATED ANNEALING RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 12 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 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 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 N7 DG A 7 N10 GIQ A 25 2.13 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 1 C5' DC A 1 C4' 0.063 REMARK 500 1 DT A 2 C6 DT A 2 N1 -0.044 REMARK 500 1 DA B 23 C2' DA B 23 C1' -0.064 REMARK 500 2 DC A 1 C5' DC A 1 C4' 0.066 REMARK 500 2 DT A 2 C6 DT A 2 N1 -0.045 REMARK 500 2 DA B 23 C2' DA B 23 C1' -0.063 REMARK 500 3 DC A 1 C5' DC A 1 C4' 0.063 REMARK 500 3 DT A 2 C6 DT A 2 N1 -0.045 REMARK 500 3 DA B 23 C2' DA B 23 C1' -0.064 REMARK 500 4 DC A 1 C5' DC A 1 C4' 0.064 REMARK 500 4 DT A 2 C6 DT A 2 N1 -0.045 REMARK 500 4 DA B 23 C2' DA B 23 C1' -0.064 REMARK 500 5 DC A 1 C5' DC A 1 C4' 0.064 REMARK 500 5 DT A 2 C6 DT A 2 N1 -0.046 REMARK 500 5 DA B 23 C2' DA B 23 C1' -0.063 REMARK 500 6 DC A 1 C5' DC A 1 C4' 0.064 REMARK 500 6 DT A 2 C6 DT A 2 N1 -0.045 REMARK 500 6 DA B 23 C2' DA B 23 C1' -0.063 REMARK 500 7 DC A 1 C5' DC A 1 C4' 0.063 REMARK 500 7 DT A 2 C6 DT A 2 N1 -0.044 REMARK 500 7 DA B 23 C2' DA B 23 C1' -0.063 REMARK 500 8 DC A 1 C5' DC A 1 C4' 0.063 REMARK 500 8 DT A 2 C6 DT A 2 N1 -0.045 REMARK 500 8 DA B 23 C2' DA B 23 C1' -0.063 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 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.4 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. = -2.5 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG B 13 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG B 13 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 13 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DA B 14 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT B 15 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG B 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 16 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG B 17 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG B 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG B 17 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG B 19 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 19 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG B 19 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA B 23 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA B 23 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG B 24 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG B 24 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG B 13 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 271 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 GIQ A 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HKB RELATED DB: PDB REMARK 900 UNMODIFIED DUPLEX DBREF 2HKC A 1 12 PDB 2HKC 2HKC 1 12 DBREF 2HKC B 13 24 PDB 2HKC 2HKC 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 7 N10 GIQ A 25 1555 1555 1.43 SITE 1 AC1 5 DG A 7 DC A 8 DG B 17 DC B 18 SITE 2 AC1 5 DG 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