HEADER DNA 06-DEC-99 1DK6 TITLE NMR STRUCTURE ANALYSIS OF THE DNA NINE BASE PAIR DUPLEX D(CATGAGTAC) TITLE 2 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, DNA EXPDTA SOLUTION NMR AUTHOR D.A.KLEWER,A.HOSKINS,V.J.DAVISSON,D.E.BERGSTROM,A.C.LIWANG REVDAT 4 16-FEB-22 1DK6 1 REMARK LINK 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,D.E.BERGSTROM, JRNL AUTH 2 A.C.LIWANG JRNL TITL NMR STRUCTURE OF A DNA DUPLEX CONTAINING NUCLEOSIDE ANALOG JRNL TITL 2 1-(2'-DEOXY-BETA-D-RIBOFURANOSYL)-3-NITROPYRROLE AND THE JRNL TITL 3 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CORMA 5.2, X-PLOR V3.840 REMARK 3 AUTHORS : LIU (CORMA), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE IS BASED ON A TOTAL OF 624 RESTRAINTS, 198 ARE REMARK 3 DERIVED FROM REMARK 3 ASSIGNED NOES, 394 ARE LOWER BOUND NOE-DERIVED RESTRAINTS TO REMARK 3 UNASSIGN 1H5*/2H5* REMARK 3 PROTONS, AND 32 ARE DIHEDRAL ANGLE RESTRAINTS REMARK 4 REMARK 4 1DK6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010151. 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, 10MM REMARK 210 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 : MARDIGRAS 5.2, NMRPIPE 1.7, VNMR REMARK 210 6.1B, SPARKY 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 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 H41 DC A 1 O6 DG B 18 1.47 REMARK 500 H21 DG A 4 O2 DC B 15 1.50 REMARK 500 O2 DC A 9 H21 DG B 10 1.52 REMARK 500 O6 DG A 4 H41 DC B 15 1.52 REMARK 500 H21 DG A 6 O2 DC B 13 1.54 REMARK 500 H1 DG A 4 N3 DC B 15 1.58 REMARK 500 H3 DT A 7 N1 DA B 12 1.59 REMARK 500 H3 DT A 3 N1 DA B 16 1.59 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 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. = -6.3 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.1 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