HEADER DNA 03-JUL-06 2HKB TITLE NMR STRUCTURE OF THE B-DNA DODECAMER CTCGGCGCCATC 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 OTHER_DETAILS: THE UNMODIFIED OLIGODEOXYNUCLEOTIDES 5'- SOURCE 4 D(CTCGGCGCCATC)-3' AND 5'-D(GATGGCGCCGAG)-3' WERE OBTAINED SOURCE 5 FROM THE MIDLAND CERTIFIED REAGENT COMPANY, AND HAD BEEN SOURCE 6 PURIFIED BY ANION EXCHANGE CHROMATOGRAPHY.; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES KEYWDS NAR1, NMR STRUCTURE, RMD CALCULATIONS, ANNEAL, NOESY, COSY, KEYWDS 2 HSQC, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR F.WANG,N.E.DEMURO,C.E.ELMQUIST,J.S.STOVER,C.J.RIZZO, AUTHOR 2 M.P.STONE REVDAT 2 24-FEB-09 2HKB 1 VERSN REVDAT 1 03-OCT-06 2HKB 0 JRNL AUTH F.WANG,N.E.DEMURO,C.E.ELMQUIST,J.S.STOVER, JRNL AUTH 2 C.J.RIZZO,M.P.STONE JRNL TITL BASE-DISPLACED INTERCALATED STRUCTURE OF THE FOOD JRNL TITL 2 MUTAGEN 2-AMINO-3-METHYLIMIDAZO[4,5-F]QUINOLINE IN JRNL TITL 3 THE RECOGNITION SEQUENCE OF THE NARI RESTRICTION JRNL TITL 4 ENZYME, A HOTSPOT FOR -2 BP 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 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 2HKB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-06. REMARK 100 THE RCSB ID CODE IS RCSB038443. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 278; 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 OLIGODEOXYNUCLEOTIDE REMARK 210 DUPLEX, 0.1 M NACL, 10 MM REMARK 210 PHOSPHATE BUFFER, AND 50 UM REMARK 210 NA2EDTA (PH 7.0), 99.996% D2O; REMARK 210 0.7 MM OLIGODEOXYNUCLEOTIDE REMARK 210 DUPLEX, 0.1 M NACL, 10 MM REMARK 210 PHOSPHATE BUFFER, AND 50 UM REMARK 210 NA2EDTA (PH 7.0), 90% H2O, 10% REMARK 210 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, 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : CP-TCI, TXI-Z, CP, QXI REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95.0, CORMA 5.2, REMARK 210 MARDIGRAS 5.2 REMARK 210 METHOD USED : DISTANCE RESTRAINT REMARK 210 CONSTRAINTS SIMULATED REMARK 210 ANNEALING RESTRAINED MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 12 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMER REMARK 210 MODELS ARE THE 10 STRUCTURES REMARK 210 WITH THE LOWEST ENERGIES 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 DA B 23 C8 DA B 23 N9 -0.066 REMARK 500 2 DA B 23 C8 DA B 23 N9 -0.066 REMARK 500 3 DA B 23 C8 DA B 23 N9 -0.067 REMARK 500 4 DA B 23 C8 DA B 23 N9 -0.067 REMARK 500 5 DA B 23 C8 DA B 23 N9 -0.066 REMARK 500 6 DA B 23 C8 DA B 23 N9 -0.067 REMARK 500 7 DA B 23 C8 DA B 23 N9 -0.067 REMARK 500 8 DA B 23 C8 DA B 23 N9 -0.067 REMARK 500 9 DA B 23 C8 DA B 23 N9 -0.066 REMARK 500 10 DA B 23 C8 DA B 23 N9 -0.067 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. = 2.9 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.2 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. = 2.9 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. = -2.7 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. = 3.5 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.8 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. = -2.6 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. = -2.8 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG B 19 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG B 19 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG B 19 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DA B 23 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA B 23 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA B 23 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 3.2 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. = -2.4 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DA A 10 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 370 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HKC RELATED DB: PDB DBREF 2HKB A 1 12 PDB 2HKB 2HKB 1 12 DBREF 2HKB B 13 24 PDB 2HKB 2HKB 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 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 163 0 0 0 0 0 0 6 0 0 0 2 END