HEADER DNA 31-JAN-95 108D TITLE THE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS TITLE 2 INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (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: CHEMICALLY SYNTHESIZED KEYWDS DNA, FLUORESCENT BIS INTERCALATOR, TOTO, BIS-THIAZOLE ORANGE EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR H.P.SPIELMANN,D.E.WEMMER,J.P.JACOBSEN REVDAT 4 13-MAR-24 108D 1 COMPND SOURCE REVDAT 3 16-FEB-22 108D 1 REMARK REVDAT 2 24-FEB-09 108D 1 VERSN REVDAT 1 03-JUN-95 108D 0 JRNL AUTH H.P.SPIELMANN,D.E.WEMMER,J.P.JACOBSEN JRNL TITL SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT JRNL TITL 2 BIS-INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY. JRNL REF BIOCHEMISTRY V. 34 8542 1995 JRNL REFN ISSN 0006-2960 JRNL PMID 7612596 JRNL DOI 10.1021/BI00027A004 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 REFINEMENT WAS BASED ON TOTAL RELAXATION MATRIX ANALYSIS OF THE REMARK 3 NOESY CROSS PEAK INTENSITIES USING THE PROGRAM MARDIGRAS. IMPROVED REMARK 3 PROCEDURES TO CONSIDER THE EXPERIMENTAL "NOISE" IN NOESY SPECTRA REMARK 3 DURING THESE CALCULATIONS HAVE BEEN EMPLOYED (LIU, H., SPIELMANN, REMARK 3 H.P., WEMMER, D.E., & JAMES, T.L. (1995) IN PREPARATION). THE NOE REMARK 3 DERIVED DISTANCE RESTRAINTS WERE APPLIED IN RESTRAINED MOLECULAR REMARK 3 DYNAMICS CALCULATIONS USING THE PROGRAM DISCOVER VERSION 2.9.5 REMARK 3 WITH MODIFIED AMBER FORCE-FIELD POTENTIALS AS IMPLEMENTED IN REMARK 3 DISCOVER. THE ROOT-MEAN-SQUARE (RMS) DEVIATION OF THE COORDINATES REMARK 3 FOR THE FORTY STRUCTURES OF THE COMPLEX WAS 1.4 ANGSTROMS REMARK 3 (INCLUDING THE DISORDERED TERMINAL DNA RESIDUES). THE COMPLEX REMARK 3 EXHIBITS TWO-FOLD SPECTROSCOPIC SYMMETRY, BUT NO SYMMETRY WAS REMARK 3 IMPOSED DURING THE REFINEMENT. DEVIATIONS FROM IDEAL TWO-FOLD REMARK 3 SYMMETRY REFLECT THE UNCERTAINTY IN THE NMR DATA. THE 40 REMARK 3 STRUCTURES ARE BASED ON 362 INTERPROTON DISTANCE RESTRAINTS FROM REMARK 3 NOE MEASUREMENTS, 22 HYDROGEN BOND DISTANCE RESTRAINTS, AND 48 REMARK 3 RESTRAINTS TO ENFORCE CHIRALITY IN THE DEOXYRIBOSE RESIDUES. THE REMARK 3 FIRST 20 STRUCTURES WERE GENERATED FROM B-FORM DNA STARTING REMARK 3 COORDINATES, AND THE REMARK 3 SECOND 20 STRUCTURES WERE GENERATED FROM A-FORM DNA REMARK 3 STARTING COORDINATES. REMARK 4 REMARK 4 108D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170020. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 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: 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 18 DG B 6 O4' DG B 6 C4' -0.062 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 DA A 5 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 5 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 5 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG A 6 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC B 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA B 5 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DA B 5 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC B 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DC A 7 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 8.2 DEGREES REMARK 500 2 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA B 5 O4' - C4' - C3' ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DA B 5 C4' - C3' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 2 DA B 5 C3' - C2' - C1' ANGL. DEV. = 7.6 DEGREES REMARK 500 2 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DA B 5 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DC B 7 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 DA A 5 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 3 DC A 7 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DA B 5 O4' - C4' - C3' ANGL. DEV. = 5.5 DEGREES REMARK 500 3 DA B 5 C4' - C3' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 3 DA B 5 C3' - C2' - C1' ANGL. DEV. = 7.9 DEGREES REMARK 500 3 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 3 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DG B 6 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 3 DC B 7 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 DA A 5 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 4 DC A 7 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 4 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 DC B 3 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 4 DA B 5 O4' - C4' - C3' ANGL. DEV. = 5.5 DEGREES REMARK 500 4 DA B 5 C4' - C3' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 4 DA B 5 C3' - C2' - C1' ANGL. DEV. = 7.9 DEGREES REMARK 500 4 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 4 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DG B 6 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 4 DC B 7 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 DA A 5 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 5 DC A 7 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 5 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 DC B 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 5 DA B 5 O4' - C4' - C3' ANGL. DEV. = 5.7 DEGREES REMARK 500 5 DA B 5 C4' - C3' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 5 DA B 5 C3' - C2' - C1' ANGL. DEV. = 8.1 DEGREES REMARK 500 5 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 383 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 DC A 1 0.07 SIDE CHAIN REMARK 500 1 DG A 2 0.06 SIDE CHAIN REMARK 500 1 DT A 4 0.09 SIDE CHAIN REMARK 500 1 DA A 5 0.08 SIDE CHAIN REMARK 500 1 DT B 4 0.08 SIDE CHAIN REMARK 500 2 DA A 5 0.06 SIDE CHAIN REMARK 500 2 DT B 4 0.11 SIDE CHAIN REMARK 500 2 DA B 5 0.06 SIDE CHAIN REMARK 500 3 DA A 5 0.07 SIDE CHAIN REMARK 500 3 DT B 4 0.11 SIDE CHAIN REMARK 500 3 DA B 5 0.06 SIDE CHAIN REMARK 500 4 DA A 5 0.08 SIDE CHAIN REMARK 500 4 DC A 7 0.08 SIDE CHAIN REMARK 500 4 DT B 4 0.11 SIDE CHAIN REMARK 500 4 DA B 5 0.05 SIDE CHAIN REMARK 500 5 DA A 5 0.08 SIDE CHAIN REMARK 500 5 DC A 7 0.08 SIDE CHAIN REMARK 500 5 DT B 4 0.10 SIDE CHAIN REMARK 500 5 DA B 5 0.08 SIDE CHAIN REMARK 500 5 DC B 7 0.08 SIDE CHAIN REMARK 500 6 DC A 1 0.07 SIDE CHAIN REMARK 500 6 DG A 2 0.09 SIDE CHAIN REMARK 500 6 DA A 5 0.09 SIDE CHAIN REMARK 500 6 DC A 7 0.08 SIDE CHAIN REMARK 500 6 DT B 4 0.07 SIDE CHAIN REMARK 500 6 DA B 5 0.13 SIDE CHAIN REMARK 500 7 DC A 1 0.07 SIDE CHAIN REMARK 500 7 DG A 2 0.09 SIDE CHAIN REMARK 500 7 DA A 5 0.09 SIDE CHAIN REMARK 500 7 DC A 7 0.07 SIDE CHAIN REMARK 500 7 DT B 4 0.08 SIDE CHAIN REMARK 500 7 DA B 5 0.13 SIDE CHAIN REMARK 500 7 DC B 7 0.08 SIDE CHAIN REMARK 500 8 DC A 1 0.07 SIDE CHAIN REMARK 500 8 DG A 2 0.08 SIDE CHAIN REMARK 500 8 DT A 4 0.08 SIDE CHAIN REMARK 500 8 DA A 5 0.07 SIDE CHAIN REMARK 500 8 DT B 4 0.08 SIDE CHAIN REMARK 500 8 DA B 5 0.06 SIDE CHAIN REMARK 500 8 DC B 7 0.09 SIDE CHAIN REMARK 500 9 DC A 1 0.07 SIDE CHAIN REMARK 500 9 DG A 2 0.08 SIDE CHAIN REMARK 500 9 DA A 5 0.07 SIDE CHAIN REMARK 500 9 DT B 4 0.09 SIDE CHAIN REMARK 500 9 DA B 5 0.06 SIDE CHAIN REMARK 500 9 DG B 6 0.08 SIDE CHAIN REMARK 500 9 DC B 7 0.07 SIDE CHAIN REMARK 500 10 DC A 1 0.07 SIDE CHAIN REMARK 500 10 DG A 2 0.09 SIDE CHAIN REMARK 500 10 DA A 5 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 207 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TOT A 9 DBREF 108D A 1 8 PDB 108D 108D 1 8 DBREF 108D B 1 8 PDB 108D 108D 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 HET TOT A 9 115 HETNAM TOT 1,1-(4,4,8,8-TETRAMETHYL-4,8-DIAZAUNDECAMETHYLENE)-BIS- HETNAM 2 TOT 4-3-METHYL-2,3-DIHYDRO-(BENZO-1,3-THIAZOLE)-2- HETNAM 3 TOT METHYLIDENE)-QUINOLINIUM FORMUL 3 TOT C49 H58 N6 S2 4+ SITE 1 AC1 8 DC A 3 DT A 4 DA A 5 DG A 6 SITE 2 AC1 8 DC B 3 DT B 4 DA B 5 DG B 6 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