HEADER DNA 15-NOV-00 1G7Z TITLE NMR SOLUTION STRUCTURE OF D(CGCTAGCG)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PHOSPHORAMADITES ON SOLID SUPPORT KEYWDS DNA, TOTO, C13 DYNAMICS, CONFORMATIONAL EXCHANGE, PHOSPHATE KEYWDS 2 CONFORMATION, DEOXYRIBOSE CONFORMATION, HELICAL PARAMETER, ORDER KEYWDS 3 PARAMETER EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.J.ISAACS,H.P.SPIELMANN REVDAT 4 23-FEB-22 1G7Z 1 REMARK REVDAT 3 24-FEB-09 1G7Z 1 VERSN REVDAT 2 01-APR-03 1G7Z 1 JRNL REVDAT 1 28-MAR-01 1G7Z 0 JRNL AUTH R.J.ISAACS,H.P.SPIELMANN JRNL TITL RELATIONSHIP OF DNA STRUCTURE TO INTERNAL DYNAMICS: JRNL TITL 2 CORRELATION OF HELICAL PARAMETERS FROM NOE-BASED NMR JRNL TITL 3 SOLUTION STRUCTURES OF D(GCGTACGC)(2) AND D(CGCTAGCG)(2) JRNL TITL 4 WITH (13)C ORDER PARAMETERS IMPLIES CONFORMATIONAL COUPLING JRNL TITL 5 IN DINUCLEOTIDE UNITS. JRNL REF J.MOL.BIOL. V. 307 525 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11254380 JRNL DOI 10.1006/JMBI.2001.4498 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.P.SPIELMANN REMARK 1 TITL DYNAMICS OF A BIS-INTERCALATOR DNA COMPLEX BY 1H-DETECTED REMARK 1 TITL 2 NATURAL ABUNDANCE 13C NMR SPECTROSCOPY REMARK 1 REF BIOCHEMISTRY V. 37 16863 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI980789E REMARK 1 REFERENCE 2 REMARK 1 AUTH H.P.SPIELMANN,D.E.WEMMER,J.P.JACOBSEN REMARK 1 TITL SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT REMARK 1 TITL 2 BIS-INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY. REMARK 1 REF BIOCHEMISTRY V. 34 8542 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1B, DISCOVER 2.98 REMARK 3 AUTHORS : VARIAN (VNMR), MSI (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 540 RESTRAINTS, 518 ARE NOE-DERIVED DISTANCE CONSTRAINTS AND 22 REMARK 3 DISTANCE RESTRAINTS FROM HYDROGEN BONDS. REMARK 4 REMARK 4 1G7Z COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-00. REMARK 100 THE DEPOSITION ID IS D_1000012347. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NACL(100MM),PO4 REMARK 210 -(20MM),NAN3(10MM),EDTA(0.1MM) REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 4 MM DNA DUPLEX REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98.0, MARDIGRAS 3.2, REMARK 210 DISCOVER 2.98 REMARK 210 METHOD USED : THE RANDMARDI PROCEDURE OF THE REMARK 210 COMPLETE RELAXATION MATRIX REMARK 210 ANALYSIS METHOD, MARDIGRAS, WAS REMARK 210 USED TO CALCULATE INTERPROTON REMARK 210 DISTANCE BOUNDS FROM THE REMARK 210 INTEGRATED NOESY CROSS-PEAK REMARK 210 INTENSITIES. THESE DISTANCE REMARK 210 BOUNDS WERE THEN USED AS REMARK 210 RESTRAINTS IN AN RMD PROCEDURE REMARK 210 TO YIELD 20 STRUCTURES. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 12 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: 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. = 2.6 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 6 C5' - C4' - O4' ANGL. DEV. = 9.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 8.7 DEGREES REMARK 500 1 DC A 7 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC B 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = 8.9 DEGREES REMARK 500 1 DC B 7 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 6 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 9.0 DEGREES REMARK 500 2 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC B 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA B 5 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG B 6 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 2 DG B 6 O4' - C1' - N9 ANGL. DEV. = 9.8 DEGREES REMARK 500 2 DC B 7 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DG B 8 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG A 6 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 9.1 DEGREES REMARK 500 3 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DC B 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DA B 5 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DG B 6 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 3 DG B 6 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 3 DG B 6 O4' - C1' - N9 ANGL. DEV. = 9.8 DEGREES REMARK 500 3 DC B 7 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 DG A 6 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 4 DG A 6 O4' - C1' - N9 ANGL. DEV. = 9.3 DEGREES REMARK 500 4 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 4 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 DC B 1 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DG B 6 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 4 DG B 6 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 4 DG B 6 O4' - C1' - N9 ANGL. DEV. = 10.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 260 ANGLE DEVIATIONS. 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 1 DG A 2 0.07 SIDE CHAIN REMARK 500 1 DT A 4 0.07 SIDE CHAIN REMARK 500 1 DG B 2 0.08 SIDE CHAIN REMARK 500 1 DT B 4 0.07 SIDE CHAIN REMARK 500 2 DG A 2 0.08 SIDE CHAIN REMARK 500 2 DT A 4 0.09 SIDE CHAIN REMARK 500 2 DA A 5 0.05 SIDE CHAIN REMARK 500 2 DG B 2 0.07 SIDE CHAIN REMARK 500 2 DT B 4 0.08 SIDE CHAIN REMARK 500 3 DG A 2 0.10 SIDE CHAIN REMARK 500 3 DT A 4 0.07 SIDE CHAIN REMARK 500 3 DG B 2 0.07 SIDE CHAIN REMARK 500 3 DT B 4 0.09 SIDE CHAIN REMARK 500 4 DG A 2 0.07 SIDE CHAIN REMARK 500 4 DT A 4 0.09 SIDE CHAIN REMARK 500 4 DA A 5 0.06 SIDE CHAIN REMARK 500 4 DG B 2 0.09 SIDE CHAIN REMARK 500 4 DT B 4 0.08 SIDE CHAIN REMARK 500 5 DG A 2 0.10 SIDE CHAIN REMARK 500 5 DT A 4 0.09 SIDE CHAIN REMARK 500 5 DA A 5 0.05 SIDE CHAIN REMARK 500 5 DG B 2 0.07 SIDE CHAIN REMARK 500 5 DT B 4 0.08 SIDE CHAIN REMARK 500 6 DG A 2 0.08 SIDE CHAIN REMARK 500 6 DT A 4 0.09 SIDE CHAIN REMARK 500 6 DA A 5 0.06 SIDE CHAIN REMARK 500 6 DG B 2 0.09 SIDE CHAIN REMARK 500 6 DT B 4 0.08 SIDE CHAIN REMARK 500 7 DG A 2 0.07 SIDE CHAIN REMARK 500 7 DT A 4 0.07 SIDE CHAIN REMARK 500 7 DT B 4 0.11 SIDE CHAIN REMARK 500 8 DG A 2 0.07 SIDE CHAIN REMARK 500 8 DT A 4 0.07 SIDE CHAIN REMARK 500 8 DA A 5 0.05 SIDE CHAIN REMARK 500 8 DG B 2 0.09 SIDE CHAIN REMARK 500 8 DT B 4 0.07 SIDE CHAIN REMARK 500 9 DG A 2 0.07 SIDE CHAIN REMARK 500 9 DT A 4 0.09 SIDE CHAIN REMARK 500 9 DG B 2 0.09 SIDE CHAIN REMARK 500 9 DT B 4 0.09 SIDE CHAIN REMARK 500 10 DG A 2 0.07 SIDE CHAIN REMARK 500 10 DT A 4 0.07 SIDE CHAIN REMARK 500 10 DA A 5 0.05 SIDE CHAIN REMARK 500 10 DG B 2 0.08 SIDE CHAIN REMARK 500 10 DT B 4 0.07 SIDE CHAIN REMARK 500 11 DG A 2 0.07 SIDE CHAIN REMARK 500 11 DT A 4 0.10 SIDE CHAIN REMARK 500 11 DG B 2 0.07 SIDE CHAIN REMARK 500 11 DT B 4 0.08 SIDE CHAIN REMARK 500 12 DG A 2 0.10 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 89 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G80 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF D(GCGTACGC)2 REMARK 900 RELATED ID: 108D RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF D(CGCTAGCG)2 WITH TOTO REMARK 900 RELATED ID: 203D RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF D(GCGTACGC)2 WITH HMT REMARK 900 RELATED ID: 204D RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF D(GCGTACGC)2 WITH HMT DBREF 1G7Z A 1 8 PDB 1G7Z 1G7Z 1 8 DBREF 1G7Z B 1 8 PDB 1G7Z 1G7Z 1 8 SEQRES 1 A 8 DC DG DC DT DA DG DC DG SEQRES 1 B 8 DC DG DC DT DA DG DC 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 MODEL 1