HEADER DNA 06-DEC-99 1DK9 TITLE SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG) 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*TP*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, DUPLEX EXPDTA SOLUTION NMR AUTHOR D.A.KLEWER,A.HOSKINS,V.J.DAVISSON,D.E.BERGSTROM,A.C.LIWANG REVDAT 5 16-FEB-22 1DK9 1 REMARK REVDAT 4 24-FEB-09 1DK9 1 VERSN REVDAT 3 01-APR-03 1DK9 1 JRNL REVDAT 2 03-NOV-00 1DK9 1 JRNL REMARK REVDAT 1 16-DEC-99 1DK9 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 : X-PLOR V3.840 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010154. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 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 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 7.1, VNMR 6.1B, PIPP REMARK 210 4.2.7 REMARK 210 METHOD USED : NULL 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 H21 DG A 6 O2 DC B 13 1.40 REMARK 500 H21 DG A 4 O2 DC B 15 1.47 REMARK 500 O2 DC A 1 H21 DG B 18 1.48 REMARK 500 O2 DC A 9 H21 DG B 10 1.50 REMARK 500 O6 DG A 4 H41 DC B 15 1.50 REMARK 500 H41 DC A 9 O6 DG B 10 1.54 REMARK 500 H1 DG A 6 N3 DC B 13 1.54 REMARK 500 H1 DG A 4 N3 DC B 15 1.55 REMARK 500 N1 DA A 8 H3 DT B 11 1.56 REMARK 500 N1 DA A 5 H3 DT B 14 1.56 REMARK 500 N1 DA A 2 H3 DT B 17 1.58 REMARK 500 O6 DG A 6 H41 DC B 13 1.58 REMARK 500 N3 DC A 1 H1 DG B 18 1.58 REMARK 500 O4 DT A 7 H61 DA B 12 1.59 REMARK 500 H3 DT A 7 N1 DA B 12 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 7 C5 DT A 7 C7 0.046 REMARK 500 DT B 17 C5 DT B 17 C7 0.038 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 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC A 9 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DG B 10 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 7.7 DEGREES REMARK 500 DT B 11 C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES REMARK 500 DA B 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 16 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG B 18 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DK6 RELATED DB: PDB REMARK 900 RESIDUE 14 IS REPLACED BY 3-NITROPYRROLE DBREF 1DK9 A 1 9 PDB 1DK9 1DK9 1 9 DBREF 1DK9 B 10 18 PDB 1DK9 1DK9 10 18 SEQRES 1 A 9 DC DA DT DG DA DG DT DA DC SEQRES 1 B 9 DG DT DA DC DT DC DA DT 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