HEADER DNA 06-DEC-99 1DK6 TITLE NMR STRUCTURE ANALYSIS OF THE DNA NINE BASE PAIR DUPLEX TITLE 2 D(CATGAGTAC) D(GTAC(NP3)CATG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(CP*AP*TP*GP*AP*GP*TP*AP*CP*)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(GP*TP*AP*CP*(NP3)P*CP*AP*TP*GP*)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED KEYWDS DNA DOUBLE HELIX, 3-NITROPYRROLE, NMR EXPDTA SOLUTION NMR AUTHOR D.A.KLEWER,A.HOSKINS,V.J.DAVISSON,D.E.BERGSTROM,A.C.LIWANG REVDAT 3 24-FEB-09 1DK6 1 VERSN REVDAT 2 17-MAY-05 1DK6 3 JRNL REMARK ATOM REVDAT 1 11-JAN-00 1DK6 0 JRNL AUTH D.A.KLEWER,A.HOSKINS,P.ZHANG,V.J.DAVISSON, JRNL AUTH 2 D.E.BERGSTROM,A.C.LIWANG JRNL TITL NMR STRUCTURE OF A DNA DUPLEX CONTAINING JRNL TITL 2 NUCLEOSIDE ANALOG JRNL TITL 3 1-(2'-DEOXY-BETA-D-RIBOFURANOSYL)-3-NITROPYRROLE JRNL TITL 4 AND THE STRUCTURE OF THE UNMODIFIED CONTROL. JRNL REF NUCLEIC ACIDS RES. V. 28 4514 2000 JRNL REFN ISSN 0305-1048 JRNL PMID 11071940 JRNL DOI 10.1093/NAR/28.22.4514 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR V3.840 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 624 RESTRAINTS, 198 ARE DERIVED FROM ASSIGNED NOES, 394 ARE REMARK 3 LOWER BOUND NOE-DERIVED RESTRAINTS TO UNASSIGN 1H5*/2H5* REMARK 3 PROTONS, AND 32 ARE DIHEDRAL ANGLE RESTRAINTS REMARK 4 REMARK 4 1DK6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-99. REMARK 100 THE RCSB ID CODE IS RCSB010151. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 285 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 4.5MM DUPLEX; 100MM NACL, REMARK 210 10MM NAOP, 1MM EDTA, PH 7 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY 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 : CORMA 5.2, MARDIGRAS 5.2, REMARK 210 NMRPIPE 1.7, VNMR 6.1B, SPARKY REMARK 210 3.74 REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS 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: NULL 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 DT A 3 C5 DT A 3 C7 0.037 REMARK 500 DT B 11 C5 DT B 11 C7 0.036 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 DA A 2 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA A 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 8 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 DG B 10 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 10 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DA B 12 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DC B 15 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA B 16 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 16 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 17 C4 - C5 - C7 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -6.4 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES 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 DG A 4 0.09 SIDE_CHAIN REMARK 500 DG A 6 0.08 SIDE_CHAIN REMARK 500 DG B 10 0.10 SIDE_CHAIN REMARK 500 DC B 13 0.11 SIDE_CHAIN REMARK 500 DA B 16 0.12 SIDE_CHAIN REMARK 500 DT B 17 0.08 SIDE_CHAIN REMARK 500 DG B 18 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1DK6 A 1 9 PDB 1DK6 1DK6 1 9 DBREF 1DK6 B 10 18 PDB 1DK6 1DK6 10 18 SEQRES 1 A 9 DC DA DT DG DA DG DT DA DC SEQRES 1 B 9 DG DT DA DC NP3 DC DA DT DG HET NP3 B 14 29 HETNAM NP3 1-[2-DEOXY-RIBOFURANOSYL]-1H-[3-NITRO-PYRROL]-5'- HETNAM 2 NP3 PHOSPHATE FORMUL 2 NP3 C9 H13 N2 O8 P LINK O3' DC B 13 P NP3 B 14 1555 1555 1.62 LINK O3' NP3 B 14 P DC B 15 1555 1555 1.62 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 MASTER 134 0 1 0 0 0 0 6 0 0 0 2 END